Methods of screening for modulators of cell proliferation and methods of diagnosing cell proliferation states

ABSTRACT

Described herein are methods that can be used for diagnosis and prognosis of cellular proliferation. Also described herein are methods that can be used to screen candidate bioactive agents for the ability to modulate cellular proliferation. Additionally, methods and molecular targets (genes and their products) for therapeutic intervention in cancers are described.

FIELD OF THE INVENTION

The invention relates to the use of nucleic acids encoding the kinesinKSP and their gene products to identify modulators of cell proliferationand their use in diagnosis, prognosis and treatment of cellproliferation states and disorders, for example cancer.

BACKGROUND OF THE INVENTION

Cancer is the second-leading cause of death in industrialized nations.Effective therapeutics include the taxanes and vinca alkyloids, agentswhich act on microtubules. Microtubules are the primary structuralelement of the mitotic spindle. The mitotic spindle is responsible fordistribution of replicate copies of the genome to each of the twodaughter cells that result from cell division. It is presumed that it isthe disruption of the mitotic spindle by these drugs that results ininhibition of cancer cell division, and also induction of cancer celldeath. However, microtubules also form other types of cellularstructures, including tracks for intracellular transport in nerveprocesses. Therefore, the taxanes have side effects that limit theirusefulness. Furthermore, taxanes and vinca alkaloids specifically targetmicrotubule polymerization dynamics. There are additional dynamics ofthe mitotic spindle that these compounds do not target.

Therefore, it is desirable to identify agents and compositions which arespecific and therapeutically effective against cancer. It is furtherdesirable to identify agents and compositions which have a novelmechanism of action. It is further desirable to provide methods ofdiagnosis of hyper or hypo proliferation disorders. Additionally, it isdesirable to identify agents and compositions which modulate cellproliferation. Cell proliferation modulation is desirable in a number ofcases as discussed below, for example, for treatment of any hyper orhypo proliferation disorder, wound healing, transplantation proceduresand for use in the agricultural arena. It is thus desirable to providesuch methods of treatment. Moreover, it is desirable to provide assaysto quickly identify such agents and compositions.

SUMMARY OF THE INVENTION

Provided herein are assays for screening for bioactive agents whichaffect cell proliferation. Also provided herein are methods ofdiagnosing proliferation states in a cell which are useful foridentifying cell proliferation disorders such as cancer. Also providedare methods of prognosis and methods of treatment including treatmentfor cancer. As is further described below, a number of compositions andmethods are provided.

In one aspect, a method of screening drug candidates is provided. In oneembodiment, said method comprises providing a cell that expressesrecombinant human KSP or a fragment thereof and adding a drug candidateto said cell under conditions where the drug candidate is taken up bythe cell. The method further includes determining the effect of saiddrug candidate on the bioactivity of said recombinant human KSP. Thebioactivity of recombinant human KSP, or particularly the changes in thepresence of a drug candidate, can be determined by assays such as thosefor determining cellular proliferation, cellular viability, and cellularmorphology. In a further aspect of the invention, any changes inbioactivity of recombinant human KSP can be determined by assays fordetermining changes in the mitotic spindle, particularly inhibition ofmitosis, and ATP hydrolysis. The methods herein may also determine thebioactivity of recombinant human KSP in the presence and absence ofcandidate agents by performing assays determining the effect onapoptosis and necrosis.

The methods provided herein can be performed on single individual cellsor a population of cells. The cell can be any kind of cell including butnot limited to a lymphocyte, cancer cell or an endothelial cell. In oneaspect, wherein cancer cells are utilized, cancer growth or inhibitioncan be determined, and wherein endothelial cells are utilized,angiogenesis or inhibition thereof can be determined.

In another aspect of the invention, a method of screening for abioactive agent capable of binding to a cellular proliferation proteinis provided. Preferably, the cellular proliferation protein is human KSPor a fragment thereof. In one embodiment, said method comprisescombining said cellular proliferation protein and a candidate bioactiveagent, wherein said candidate bioactive agent is an exogenous agent, anddetermining the binding of said candidate agent to said cellularproliferation protein.

In a further aspect herein, a method of screening for a candidateprotein capable of binding to a cellular proliferation protein, whereinsaid cellular proliferation protein is KSP or a fragment thereof, isprovided. In a preferred method, said method comprises combining anucleic acid encoding said cellular proliferation protein and a nucleicacid encoding a candidate protein, wherein an identifiable marker isexpressed wherein said candidate protein binds to said cellularproliferation protein.

Also provided herein is a method for screening for a bioactive agentcapable of interfering with the binding of a cellular proliferationprotein, wherein said cellular proliferation protein is KSP or afragment thereof, and an antibody which binds to said cellularproliferation protein. In one embodiment, the method comprises combininga cellular proliferation protein, wherein said cellular proliferationprotein is KSP or fragment thereof, a candidate bioactive agent and anantibody which binds to said cellular proliferation protein anddetermining the binding of said cellular proliferation protein and saidantibody.

In a further aspect of the invention herein, a method for screening fora bioactive agent capable of modulating the activity of a cellularproliferation protein, wherein said cellular proliferation protein ishuman KSP or a fragment thereof, is provided. In one aspect, said methodcomprises combining said cellular proliferation protein and a candidatebioactive agent, wherein said candidate bioactive agent is an exogenousagent, and determining the effect of said candidate agent on theactivity of said cellular proliferation protein.

Also provided herein is a method of screening drug candidates comprisingproviding a cell that expresses KSP, adding a drug candidate to saidcell, and determining the effect of said drug candidate on theexpression of KSP. In a further aspect the method includes comparing thelevel of expression in the absence of said drug candidate to the levelof expression in the presence of said drug candidate, wherein theconcentration of said drug candidate can vary when present, and whereinsaid comparison can occur after addition or removal of the drugcandidate. In a preferred embodiment, the expression of said KSP isdecreased as a result of the introduction of the drug candidate.Preferably, the cell utilized is a tumor cell.

In a further aspect, a method of evaluating the effect of a candidatedrug on cellular proliferation (a candidate cellular proliferation drug)is provided which comprises administering said drug to a patient,removing a cell sample from said patient, and determining the expressionprofile of said cell, wherein said expression profile includes a KSPgene. In another aspect, the method includes comparing said expressionprofile to an expression profile of a healthy individual.

In another aspect herein, a method of diagnosing a hyper-proliferativedisorder in an individual is provided herein comprising determining thelevel of expression a KSP gene in an individual and comparing said levelto a standard or control level of expression, wherein an increaseindicates that the individual has a hyper-proliferative disorder, suchas, but not limited to, cancer.

Also provided herein is a method of evaluating the effect of a candidatecellular proliferation drug comprising administering said drug to apatient wherein said patient has cancer and has been identified asexpressing KSP at a level higher than an individual not having cancer,removing a cell sample from said patient, and determining the effect onKSP activity, wherein said KSP activity is mitosis.

In the methods provided herein, the cells can come from a variety ofsources. For example, samples can be from, but are not limited to, ablood sample, a urine sample, a buccal sample, a PAP smear, cerebralspinal fluid, and any tissue including, breast tissue, lung tissue andcolon tissue. In one embodiment, the patient has cancer.

Also provided herein is a method for inhibiting cellular proliferation,said method comprising administering to a cell a composition comprisingan antibody to KSP, wherein said antibody is conjugated to a ligand. Inone aspect, the ligand of the antibody is tumor cell specific. Inanother aspect, the ligand facilitates said antibody entry to said cell.Moreover, the antibody can be a humanized antibody. The methods ofinhibition can be performed in vitro on cells or in vivo on anindividual. In one embodiment, the cells are cancerous. In a furtherembodiment, the individual has cancer. Another method of inhibitingcellular proliferation in a cell or individual is provided herein whichcomprises administering to a cell or individual a composition comprisingantisense molecules to KSP.

In yet another embodiment herein, a method for inhibiting cellularproliferation is provided which comprises administering to a cell acomposition comprising an inhibitor of KSP. In one embodiment, theinhibitor is of human KSP or a fragment thereof. In one embodiment, theinhibitor is specific to human KSP. In one embodiment, KSP inhibitorsare any agent which disrupts or inhibits KSP activity as furtherdescribed herein. In one aspect of the invention, the inhibitor of KSPis a small molecule as further defined herein. Generally, smallmolecules have a molecular weight of between 50 kD and 2000 kD, and insome cases, less than 1500 kD, or less than 1000 kD or less than 500 kD.Examples of KSP inhibitors include but are not limited to smallmolecules, ribozymes, antisense molecules and antibodies. KSP inhibitorsare further described herein and in the application filed Oct. 27, 1999,entitled Methods and Compositions Utilizing Quinazolinones (serialnumber not yet received, named inventor Jeffrey T. Finer), incorporatedby reference in its entirety. The composition which is administered to acell further comprises an acceptable pharmaceutical carrier in oneembodiment. The composition can have a variety of formulations,including, but not limited to those for parental, oral or topicaladministration.

The methods of inhibiting cellular proliferation can be performed invitro or in vivo. More particularly, the compositions can beadministered to cells in vitro or in an individual. The individual mayhave a disease or be at risk for disease. Disease states which can betreated by the methods herein are further described below. In one case,the individual has cancer or is at risk for restenosis. The cell can beany cell, preferably a cancer cell. Other preferred cell types includebut are not limited to endothelial cells and metastatic cancer cells. Inone embodiment, the method of inhibiting by the KSP inhibitor is bydisruption of mitosis or induction of apoptosis.

In a further aspect of the invention, a biochip comprising a nucleicacid segment from KSP, wherein said biochip comprises fewer than 1000nucleic acid probes, is provided. Methods of screening and diagnosingconditions with said biochip are also provided herein.

Other aspects of the invention will become apparent to the skilledartisan by the following description of the invention.

DETAILED DESCRIPTION OF THE FIGURES

FIG. 1 shows a cDNA sequence for human KSP, GenBank accession numberX85137, wherein the start and stop codons are shown underlined and inbold, beginning at positions 11 and 3182, respectively.

FIG. 2 shows an amino acid sequence encoding human KSP.

FIG. 3 shows a nucleic acid sequence encoding a fragment of KSP, termedKSPL360 herein. Portions differing from the sequences of FIGS. 1 and 2are indicated in bold typeface and are underlined. Residues at theC-terminus include a myc epitope and a 6-histidine tag.

FIG. 4 shows an amino acid sequence encoding KSPL360.

FIG. 5 shows a nucleic acid sequence encoding a fragment of KSP, termedKSP-K491 herein. Portions differing from the sequences of FIGS. 1 and 2are indicated in bold typeface and are underlined. Residues at theC-terminus include a myc epitope and a 6-histidine tag.

FIG. 6 shows an amino acid sequence encoding KSP-K491.

FIG. 7 shows a nucleic acid sequence encoding a fragment of KSP, termedKSP-S553 herein. Portions differing from the sequences of FIGS. 1 and 2are indicated in bold typeface and are underlined. Residues at theC-terminus include a myc epitope and a 6-histidine tag.

FIG. 8 shows an amino acid sequence encoding KSP-S553.

FIG. 9 shows a nucleic acid sequence encoding a fragment of KSP, termedKSP-K368 herein. Portions differing from the sequences of FIGS. 1 and 2are indicated in bold typeface and are underlined.

FIG. 10 shows an amino acid sequence encoding KSP-K368.

FIG. 11 is a graph showing KSP mRNA levels in matched normal and tumortissue from breast, lung and colon. mRNA levels were measured byquantitative PCR relative to a standard. The relative magnitudes ofoverexpression in each tumor sample relative to the matched normaltissue are displayed above each pair. All values are normalized to thelevel of KSP mRNA expression observed in cultured HeLa cells.

DETAILED DESCRIPTION OF THE INVENTION

Provided herein are assays for screening for bioactive agents whichaffect cell proliferation. Also provided herein are methods ofdiagnosing proliferation states in a cell which are useful foridentifying cell proliferation disorders such as cancer. Also providedare methods of prognosis and methods of treatment including treatmentfor cancer. As is further described below, a number of compositions andmethods are provided.

In one aspect, the assays or methods of diagnosis provided hereininclude the use of a cellular proliferation protein or nucleic acid. Theterms “cell proliferation” and “cellular proliferation” are used hereininterchangeably. Additionally, the cellular proliferation protein andnucleic acid can be referred to herein as “cellular proliferationsequences” wherein the context will indicate whether the sequence is anamino acid sequence, nucleic acid sequence, or either.

In a preferred embodiment, the cellular proliferation sequence is KSP.KSP belongs to an evolutionarily conserved kinesin subfamily of plusend-directed microtubule motors that assemble into bipolar homotetramersconsisting of antiparallel homodimers. During mitosis KSP associateswith microtubules of the mitotic spindle. Microinjection of antibodydirected against KSP into cells prevents spindle pole separation duringprometaphase, giving rise to monopolar spindles and causing mitoticarrest. KSP and related kinesins bundle antiparallel microtubules andslide them relative to one another, thus forcing the two spindle polesapart. KSP may also mediate in anaphase B spindle elongation andfocussing of microtubules at the spindle pole.

Human KSP has been reported on (also termed HsEg5). Galgio, et al., J.Cell Biol., 135(2):399-414 (1996); Kaiser, et al., JBC, 274(27):18925-31(1999); Blangy, et al., Cell, 83:1159-69 (1995); Blangy, et al., J Biol.Chem., 272:19418-24 (1997); Slangy, et al., Cell Motil Cytoskeleton,40:174-82 (1998); Whitehead, et al., Arthritis Rheum., 39:1635-42(1996); GenBank accession numbers: X85137, NM_(—)004523 and U37426.Moreover, a fragment of the KSP gene (TRIPS) has been reported on. Lee,et al., Mol. Endocrinol., 9:243-54 (1995); GenBank accession numberL40372. Also see, Whitehead and Rattner, J. Cell Sci., 111:2551-61(1998).

Xenopus KSP homologs (Eg5) have also been reported on. Walczak, et al.,Curr Biol., 8(16):903-13 (1998); Le Guellec, et al., Mol. Cell. Biol.,11(6):3395-8 (1991); Sawin, et al., Nature, 359:540-3 (1992); Sawin andMitchison, Mol Biol Cell, 5:217-26 (1994); Sawin and Mitchison, PNAS,92:4289-93 (1995); Kapoor and Mitchison, PNAS, 96:9106-11 (1999);Lockhart and Cross, Biochemistry, 35(7):2365-73 (1996); Crevel, et al,J. Mol. Biol., 273:160-170 (1997). Additionally, DrosophilaKLP61F/KRP130 has been reported on. Heck, et al., J Cell Biol,123:665-79 (1993); Cole, et al., J. Biol. Chem., 269(37):22913-6 (1994);Barton, et al., Mol. Biol. Cell, 6:1563-74 (1995).

In the preferred embodiment herein, a sequence as shown in the figuresis utilized. As indicated herein, in some embodiments a fragment of KSPis utilized. Preferred protein fragments are shown in FIGS. 2, 4, 6, and8. In one embodiment, the cellular proliferation fragment shown in FIG.4 is preferred. Preferred fragments of KSP have kinesin activity asfurther described below. Moreover, in one embodiment, KSP peptides orfragments have at least one, and preferably at least two epitope tags.In a preferred embodiment, a KSP fragment comprises a myc epitope and ahistidine tag.

In another preferred embodiment herein, the cellular proliferationprotein is non-glycosylated. For example, in one embodiment the proteinis, for example, human, expressed in bacteria, for example, E. Coli.Moreover, phosphorylation and/or methylation of KSP as used herein maydiffer from KSP as found in its native form within a cell.

Thus, while it is preferred that the cellular proliferation sequencesare from humans, sequences from other organisms may be useful in animalmodels of disease and drug evaluation; thus, in alternative embodiments,other sequences are provided such as from vertebrates, includingmammals, including rodents (rats, mice, hamsters, guinea pigs, etc.),primates, farm animals (including sheep, goats, pigs, cows, horses,etc), Xenopus, and Drosophila.

In another embodiment, the sequences are naturally-occurring allelicvariants of the sequences set forth in the figures. In anotherembodiment, the sequences are sequence variants as further describedherein.

In one embodiment, a cellular proliferation sequence can be initiallyidentified by substantial nucleic acid and/or amino acid sequencehomology to the cellular proliferation sequences outlined herein. Suchhomology can be based upon the overall nucleic acid or amino acidsequence, and is generally determined as outlined below, using eitherhomology programs or hybridization conditions.

Thus, in one embodiment, a nucleic acid is a “cellular proliferationnucleic acid” if the overall homology of the nucleic acid sequence tothe nucleic acid sequences of FIG. 1, 3, 5, 7 or 9 (the nucleic acidfigures) is preferably greater than about 75%, more preferably greaterthan about 80%, even more preferably greater than about 85% and mostpreferably greater than 90%. In some embodiments the homology will be ashigh as about 93 to 95 or 98%. Homology as used herein is in referenceto sequence similarity or identity, with identity being preferred. Thishomology will be determined using standard techniques known in the art,including, but not limited to, the local homology algorithm of Smith &Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignmentalgorithm of Needleman & Wunsch, J. Mol. Biool. 48:443 (1970), by thesearch for similarity method of Pearson & Lipman, PNAS USA 85:2444(1988), by computerized implementations of these algorithms (GAP,BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package,Genetics Computer Group, 575 Science Drive, Madison, Wis.), the Best Fitsequence program described by Devereux et al., Nucl. Acid Res.12:387-395 (1984), preferably using the default settings, or byinspection.

One example of a useful algorithm is PILEUP. PILEUP creates a multiplesequence alignment from a group of related sequences using progressive,pairwise alignments. It can also plot a tree showing the clusteringrelationships used to create the alignment. PILEUP uses a simplificationof the progressive alignment method of Feng & Doolittle, J. Mol. Evol.35:351-360 (1987); the method is similar to that described by Higgins &Sharp CABIOS 5:151-153 (1989). Useful PILEUP parameters including adefault gap weight of 3.00, a default gap length weight of 0.10, andweighted end gaps.

Another example of a useful algorithm is the BLAST algorithm, describedin Altschul et al., J. Mol. Biol. 215, 403-410, (1990) and Karlin etal., PNAS USA 90:5873-5787 (1993). A particularly useful BLAST programis the WU-BLAST-2 program which was obtained from Altschul et al.,Methods in Enzymology, 266: 460-480 (1996);http://blast.wustl/edu/blast/REACRCE.html). WU-BLAST-2 uses severalsearch parameters, most of which are set to the default values. Theadjustable parameters are set with the following values: overlap span=1,overlap fraction=0.125, word threshold (T)=11. The HSP S and HSP S2parameters are dynamic values and are established by the program itselfdepending upon the composition of the particular sequence andcomposition of the particular database against which the sequence ofinterest is being searched; however, the values may be adjusted toincrease sensitivity. A % amino acid sequence identity value isdetermined by the number of matching identical residues divided by thetotal number of residues of the “longer” sequence in the aligned region.The “longer” sequence is the one having the most actual residues in thealigned region (gaps introduced by WU-Blast-2 to maximize the alignmentscore are ignored).

Thus, “percent (%) nucleic acid sequence identity” is defined as thepercentage of nucleotide residues in a candidate sequence that areidentical with the nucleotide residues of the sequence shown in thenucleic acid figures. A preferred method utilizes the BLASTN module ofWU-BLAST-2 set to the default parameters, with overlap span and overlapfraction set to 1 and 0.125, respectively.

The alignment may include the introduction of gaps in the sequences tobe aligned. In addition, for sequences which contain either more orfewer nucleosides than those of the nucleic acid figures, it isunderstood that the percentage of homology will be determined based onthe number of homologous nucleosides in relation to the total number ofnucleosides. Thus, for example, homology of sequences shorter than thoseof the sequences identified herein and as discussed below, will bedetermined using the number of nucleosides in the shorter sequence.

In one embodiment, the cellular proliferation nucleic acid is determinedthrough hybridization studies. Thus, for example, nucleic acids whichhybridize under high stringency to the nucleic acid sequences identifiedin the figures, or a complement, are considered a cellular proliferationsequence in one embodiment herein. High stringency conditions are knownin the art; see for example Maniatis et al., Molecular Cloning: ALaboratory Manual, 2d Edition, 1989, and Short Protocols in MolecularBiology, ed. Ausubel, et al., both of which are hereby incorporated byreference. Stringent conditions are sequence-dependent and will bedifferent in different circumstances. Longer sequences hybridizespecifically at higher temperatures. An extensive guide to thehybridization of nucleic acids is found in Tijssen, Techniques inBiochemistry and Molecular Biology—Hybridization with Nucleic AcidProbes, “Overview of principles of hybridization and the strategy ofnucleic acid assays” (1993). Generally, stringent conditions areselected to be about 5-10° C. lower than the thermal melting point (Tm)for the specific sequence at a defined ionic strength pH. The Tm is thetemperature (under defined ionic strength, pH and nucleic acidconcentration) at which 50% of the probes complementary to the targethybridize to the target sequence at equilibrium (as the target sequencesare present in excess, at Tm, 50% of the probes are occupied atequilibrium). Stringent conditions will be those in which the saltconcentration is less than about 1.0 M sodium ion, typically about 0.01to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 andthe temperature is at least about 30° C. for short probes (e.g. 10 to 50nucleotides) and at least about 60° C. for long probes (e.g. greaterthan 50 nucleotides). Stringent conditions may also be achieved with theaddition of destabilizing agents such as formamide.

In another embodiment, less stringent hybridization conditions are used;for example, moderate or low stringency conditions may be used, as areknown in the art; see Maniatis and Ausubel, supra, and Tijssen, supra.

In addition, in one embodiment the cellular proliferation nucleic acidsequences of the invention are fragments of larger genes, i.e. they arenucleic acid segments. “Genes” in this context includes coding regions,non-coding regions, and mixtures of coding and non-coding regions.Accordingly, as will be appreciated by those in the art, using thesequences provided herein, additional sequences of the cellularproliferation genes can be obtained, using techniques well known in theart for cloning either longer sequences or the full length sequences;see Maniatis et al., and Ausubel, et al., supra, hereby expresslyincorporated by reference.

Once the cellular proliferation nucleic acid is identified, it can becloned and, if necessary, its constituent parts recombined to form theentire cellular proliferation nucleic acid. Once isolated from itsnatural source, e.g., contained within a plasmid or other vector orexcised therefrom as a linear nucleic acid segment, the recombinantcellular proliferation nucleic acid can be further-used as a probe toidentify and isolate other cellular proliferation nucleic acids, forexample additional coding regions. It can also be used as a “precursor”nucleic acid to make modified or variant cellular proliferation nucleicacids and proteins. “Recombinant” as used herein refers to a nucleicacid or protein which is not in its native state. For example, thenucleic acid can be genetically engineered, isolated, inserted into aman-made vector or be in a cell wherein it is not natively expressed inorder to be considered recombinant.

In another aspect, the cellular proliferation nucleic acid and proteinsequences are differentially expressed in cells having varying states ofcellular proliferation, including cancer cells which over proliferatecompared to non cancerous cells. As outlined below, cellularproliferation sequences include those that are up-regulated (i.e.expressed at a higher level) during cellular proliferation, as well asthose that are down-regulated (i.e. expressed at a lower level) incellular proliferation. In a preferred embodiment, the cellularproliferation sequences are upregulated during cellular proliferation intheir native state, ie., without the administration of modulators ortherapeutics.

The term “nucleic acid” refers to deoxyribonucleotides orribonucleotides and polymers thereof in either single- ordouble-stranded form. Unless specifically limited, the term encompassesnucleic acids containing known analogues of natural nucleotides whichhave similar binding properties as the reference nucleic acid and aremetabolized in a manner similar to naturally occurring nucleotides.Unless otherwise indicated, a particular nucleic acid sequence alsoimplicitly encompasses conservatively modified variants thereof (e.g.,degenerate codon substitutions) and complementary sequences and as wellas the sequence explicitly indicated. Specifically, degenerate codonsubstitutions may be achieved by generating sequences in which the thirdposition of one or more selected (or all) codons is substituted withmixed-base and/or deoxyinosine residues (Batzer et al., Nucleic AcidRes. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608(1985); Cassol et al., 1992; Rossolini et al., Mol. Cell. Probes 8:91-98(1994)). The term nucleic acid is used interchangeably with gene, cDNA,and mRNA encoded by a gene.

The cellular proliferation nucleic acids of the present invention areused in several ways. In a preferred embodiment, cellular proliferationnucleic acids encoding cellular proliferation proteins are used to makea variety of expression vectors to express cellular proliferationproteins which can then be used in screening assays, as described below.The expression vectors may be either self-replicating extrachromosomalvectors or vectors which integrate into a host genome. Generally, theseexpression vectors include transcriptional and translational regulatorynucleic acid operably linked to the nucleic acid encoding the cellularproliferation protein. The term “control sequences” refers to DNAsequences necessary for the expression of an operably linked codingsequence in a particular host organism. The control sequences that aresuitable for prokaryotes, for example, include a promoter, optionally anoperator sequence, and a ribosome binding site. Eukaryotic cells areknown to utilize promoters, polyadenylation signals, and enhancers.

Nucleic acid is “operably linked” when it is placed into a functionalrelationship with another nucleic acid sequence. For example, DNA for apresequence or secretory leader is operably linked to DNA for apolypeptide if it is expressed as a preprotein that participates in thesecretion of the polypeptide; a promoter or enhancer is operably linkedto a coding sequence if it affects the transcription of the sequence; ora ribosome binding site is operably linked to a coding sequence if it ispositioned so as to facilitate translation. Generally, “operably linked”means that the DNA sequences being linked are contiguous, and, in thecase of a secretory leader, contiguous and in reading phase. However,enhancers do not have to be contiguous. Linking is accomplished byligation at convenient restriction sites. If such sites do not exist,the synthetic oligonucleotide adaptors or linkers are used in accordancewith conventional practice. The transcriptional and translationalregulatory nucleic acid will generally be appropriate to the host cellused to express the cellular proliferation protein; for example,transcriptional and translational regulatory nucleic acid sequences fromBacillus are preferably used to express the cellular proliferationprotein in Bacillus. Numerous types of appropriate expression vectors,and suitable regulatory sequences are known in the art for a variety ofhost cells.

In general, the transcriptional and translational regulatory sequencesmay include, but are not limited to, promoter sequences, ribosomalbinding sites, transcriptional start and stop sequences, translationalstart and stop sequences, and enhancer or activator sequences. In apreferred embodiment, the regulatory sequences include a promoter andtranscriptional start and stop sequences.

Promoter sequences encode either constitutive or inducible promoters.The promoters may be either naturally occurring promoters or hybridpromoters. Hybrid promoters, which combine elements of more than onepromoter, are also known in the art, and are useful in the presentinvention.

In addition, the expression vector may comprise additional elements. Forexample, the expression vector may have two replication systems, thusallowing it to be maintained in two organisms, for example in mammalianor insect cells for expression and in a procaryotic host for cloning andamplification. Furthermore, for integrating expression vectors, theexpression vector contains at least one sequence homologous to the hostcell genome, and preferably two homologous sequences which flank theexpression construct. The integrating vector may be directed to aspecific locus in the host cell by selecting the appropriate homologoussequence for inclusion in the vector. Constructs for integrating vectorsare well known in the art.

In addition, in a preferred embodiment, the expression vector contains aselectable marker gene to allow the selection of transformed host cells.Selection genes are well known in the art and will vary with the hostcell used.

The cellular proliferation proteins of the present invention can beproduced by culturing a host cell transformed with an expression vectorcontaining nucleic acid encoding a cellular proliferation protein, underthe appropriate conditions to induce or cause expression of the cellularproliferation protein. The conditions appropriate for cellularproliferation protein expression will vary with the choice of theexpression vector and the host cell, and will be easily ascertained byone skilled in the art through routine experimentation. For example, theuse of constitutive promoters in the expression vector will requireoptimizing the growth and proliferation of the host cell, while the useof an inducible promoter requires the appropriate growth conditions forinduction. In addition, in some embodiments, the timing of the harvestis important. For example, the baculoviral systems used in insect cellexpression are lytic viruses, and thus harvest time selection can becrucial for product yield.

Appropriate host cells include yeast, bacteria, archaebacteria, fungi,and insect and animal cells, including mammalian cells. Of particularinterest are Drosophila melangaster cells, Saccharomyces cerevisiae andother yeasts, E. coli, Bacillus subtilis, Sf9 cells, C129 cells, 293cells, Neurospora, BHK, CHO, COS, HeLa cells, THP1 cell line (amacrophage cell line) and human cells and cell lines.

In one embodiment, the cellular proliferation proteins are expressed inmammalian cells. Mammalian expression systems are also known in the art,and include retroviral systems. A preferred expression vector system isa retroviral vector system such as is generally described inPCT/US97/01019 and PCT/US97/01048, both of which are hereby expresslyincorporated by reference. Of particular use as mammalian promoters arethe promoters from mammalian viral genes, since the viral genes areoften highly expressed and have a broad host range. Examples include theSV40 early promoter, mouse mammary tumor virus LTR promoter, adenovirusmajor late promoter, herpes simplex virus promoter, and the CMVpromoter. Typically, transcription termination and polyadenylationsequences recognized by mammalian cells are regulatory regions located3′ to the translation stop codon and thus, together with the promoterelements, flank the coding sequence. Examples of transcriptionterminator and polyadenylation signals include those derived form SV40.

The methods of introducing exogenous nucleic acid into mammalian hosts,as well as other hosts, is well known in the art, and will vary with thehost cell used. Techniques include dextran-mediated transfection,calcium phosphate precipitation, polybrene mediated transfection,protoplast fusion, electroporation, viral infection, encapsulation ofthe polynucleotide(s) in liposomes, and direct microinjection of the DNAinto nuclei.

In a preferred embodiment, cellular proliferation proteins are expressedin bacterial systems. Bacterial expression systems are well known in theart. Promoters from bacteriophage may also be used and are known in theart. In addition, synthetic promoters and hybrid promoters are alsouseful; for example, the tac promoter is a hybrid of the trp and lacpromoter sequences. Furthermore, a bacterial promoter can includenaturally occurring promoters of non-bacterial origin that have theability to bind bacterial RNA polymerase and initiate transcription. Inaddition to a functioning promoter sequence, an efficient ribosomebinding site is desirable. The expression vector may also include asignal peptide sequence that provides for secretion of the cellularproliferation protein in bacteria. The protein is either secreted intothe growth media (gram-positive bacteria) or into the periplasmic space,located between the inner and outer membrane of the cell (gram-negativebacteria). The expression vector may also include an epitope tagproviding for affinity purification of the cellular proliferationprotein. The bacterial expression vector may also include a selectablemarker gene to allow for the selection of bacterial strains that havebeen transformed. Suitable selection genes include genes which renderthe bacteria resistant to drugs such as ampicillin, chloramphenicol,erythromycin, kanamycin, neomycin and tetracycline. Selectable markersalso include biosynthetic genes, such as those in the histidine,tryptophan and leucine biosynthetic pathways. These components areassembled into expression vectors. Expression vectors for bacteria arewell known in the art, and include vectors for Bacillus subtilis, E.coli, Streptococcus cremoris, and Streptococcus lividans, among others.The bacterial expression vectors are transformed into bacterial hostcells using techniques well known in the art, such as calcium chloridetreatment, electroporation, and others.

In one embodiment, cellular proliferation proteins are produced ininsect cells. Expression vectors for the transformation of insect cells,and in particular, baculovirus-based expression vectors, are well knownin the art.

In another embodiment, cellular proliferation protein is produced inyeast cells. Yeast expression systems are well known in the art, andinclude expression vectors for Saccharomyces cerevisiae, Candidaalbicans and C. maltose, Hansenula polymorpha, Kluyveromyces fragilisand K. lactic, Pichia guillerimondii and P. pastoris,Schizosaccharomyces pombe, and Yarrowia lipolytica.

The cellular proliferation protein may also be made as a fusion protein,using techniques well known in the art. Thus, for example, for thecreation of monoclonal antibodies, if the desired epitope is small, thecellular proliferation protein may be fused to a carrier protein to forman immunogen. Alternatively, the cellular proliferation protein may bemade as a fusion protein to increase expression, or for other reasons.For example, when the cellular proliferation protein is a cellularproliferation peptide, the nucleic acid encoding the peptide may belinked to other nucleic acid for expression purposes.

In one embodiment, the cellular proliferation nucleic acids, proteinsand antibodies of the invention are labeled. By “labeled” herein ismeant that a compound has at least one element, isotope or chemicalcompound attached to enable the detection of the compound. In general,labels fall into three classes: a) isotopic labels, which may beradioactive or heavy isotopes; b) immune labels, which may be antibodiesor antigens; and c) colored or fluorescent dyes. The labels may beincorporated into the cellular proliferation nucleic acids, proteins andantibodies at any position. For example, the label should be capable ofproducing, either directly or indirectly, a detectable signal. Thedetectable moiety may be a radioisotope, such as ³H, ¹⁴C, ³²P, ³⁵S, or¹²⁵I, a fluorescent or chemiluminescent compound, such as fluoresceinisothiocyanate, rhodamine, or luciferin, or an enzyme, such as alkalinephosphatase, beta-galactosidase or horseradish peroxidase. Any methodknown in the art for conjugating the antibody to the label may beemployed, including those methods described by Hunter et al., Nature,144:945 (1962); David et al., Biochemistry, 13:1014 (1974); Pain et al.,J. Immunol. Meth., 40:219 (1981); and Nygren, J. Histochem. andCytochem., 30:407 (1982).

Accordingly, the present invention also provides cellular proliferationprotein sequences. A cellular proliferation protein of the presentinvention may be identified in several ways. “Protein” in this senseincludes proteins, polypeptides, and peptides. As will be appreciated bythose in the art, the nucleic acid sequences of the invention can beused to generate protein sequences.

Also included within one embodiment of cellular proliferation proteinsare amino acid variants of the naturally occurring sequences, asdetermined herein. Preferably, the variants are preferably greater thanabout 75% homologous to the wild-type sequence, more preferably greaterthan about 80%, even more preferably greater than about 85% and mostpreferably greater than 90%. In some embodiments the homology will be ashigh as about 93 to 95 or 98%. As for nucleic acids, homology in thiscontext means sequence similarity or identity, with identity beingpreferred. This homology will be determined using standard techniquesknown in the art as are outlined above for the nucleic acid homologies.The proteins of the present invention may be shorter or longer than thewild type amino acid sequences. Thus, in a preferred embodiment,included within the definition of cellular proliferation proteins areportions or fragments of the wild type sequences. Preferred fragmentshave a binding domain to a modulating agent or antibody as discussedbelow. In addition, as outlined above, the cellular proliferationnucleic acids of the invention may be used to obtain additional codingregions, and thus additional protein sequence, using techniques known inthe art.

In one embodiment, the cellular proliferation proteins are derivative orvariant cellular proliferation proteins as compared to the wild-typesequence. That is, as outlined more fully below, the derivative cellularproliferation peptide will contain at least one amino acid substitution,deletion or insertion, with amino acid substitutions being particularlypreferred. The amino acid substitution, insertion or deletion orcombination thereof may occur at any residue within the cellularproliferation peptide. These variants ordinarily are prepared by sitespecific mutagenesis of nucleotides in the DNA encoding the cellularproliferation protein, using cassette or PCR mutagenesis or othertechniques well known in the art, to produce DNA encoding the variant,and thereafter expressing the DNA in recombinant cell culture asoutlined above. However, variant cellular proliferation proteinfragments having up to about 100-150 residues may be prepared by invitro synthesis using established techniques. Amino acid sequencevariants are characterized by the predetermined nature of the variation,a feature that sets them apart from naturally occurring allelic orinterspecies variation of the cellular proliferation protein amino acidsequence. The variants typically exhibit the same qualitative biologicalactivity as the naturally occurring analogue, although variants can alsobe selected which have modified characteristics as will be more fullyoutlined below.

While the site or region for introducing an amino acid sequencevariation is predetermined, the mutation per se need not bepredetermined. For example, in order to optimize the performance of amutation at a given site, random mutagenesis may be conducted at thetarget codon or region and the expressed cellular proliferation variantsscreened for the optimal combination of desired activity. Techniques formaking substitution mutations at predetermined sites in DNA having aknown sequence are well known, for example, M13 primer mutagenesis andPCR mutagenesis. Screening of the mutants is done using assays ofcellular proliferation protein activities.

Amino acid substitutions are typically of single residues; insertionsusually will be on the order of from about 1 to 20 amino acids, althoughconsiderably larger insertions may be tolerated. Deletions range fromabout 1 to about 20 residues, although in some cases deletions may bemuch larger.

Substitutions, deletions, insertions or any combination thereof may beused to arrive at a final derivative. Generally these changes are doneon a few amino acids to minimize the alteration of the molecule.However, larger changes may be tolerated in certain circumstances. Whensmall alterations in the characteristics of the cellular proliferationprotein are desired, substitutions are generally made in accordance withthe following chart:

CHART I Original Residue Exemplary Substitutions Ala Ser Arg Lys AsnGln, His Asp Glu Cys Ser Gln Asn Glu Asp Gly Pro His Asn, Gln Ile Leu,Val Leu Ile, Val Lys Arg, Gln, Glu Met Leu, Ile Phe Met, Leu, Tyr SerThr Thr Ser Trp Tyr Tyr Trp, Phe Val Ile, Leu

Substantial changes in function or immunological identity are made byselecting substitutions that are less conservative than those shown inChart I. For example, substitutions may be made which more significantlyaffect: the structure of the polypeptide backbone in the area of thealteration, for example the alpha-helical or beta-sheet structure; thecharge or hydrophobicity of the molecule at the target site; or the bulkof the side chain. The substitutions which in general are expected toproduce the greatest changes in the polypeptide's properties are thosein which (a) a hydrophilic residue, e.g. seryl or threonyl issubstituted for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl,phenylalanyl, valyl or alanyl; (b) a cysteine proline is substituted for(or by) any other residue; (c) a residue having an electropositive sidechain, e.g. lysyl, arginyl, or histidyl, is substituted for (or by) anelectronegative residue, e.g. glutamyl or aspartyl; or (d) a residuehaving a bulky side chain, e.g. phenylalanine, is substituted for (orby) one not having a side chain, e.g. glycine.

The variants typically exhibit the same qualitative biological activityand will elicit the same immune response as the naturally-occurringanalogue, although variants also are selected to modify thecharacteristics of the cellular proliferation proteins as needed.Alternatively, the variant may be designed such that the biologicalactivity of the cellular proliferation protein is altered.

Covalent modifications of cellular proliferation polypeptides areincluded within the scope of this invention. One type of covalentmodification includes reacting targeted amino acid residues of acellular proliferation polypeptide with an organic derivatizing agentthat is capable of reacting with selected side chains or the N- orC-terminal residues of a cellular proliferation polypeptide.Derivatization with bifunctional agents is useful, for instance, forcrosslinking cellular proliferation protein to a water-insoluble supportmatrix or surface for use in the method for purifying anti-KSPantibodies or screening assays, as is more fully described below.Commonly used crosslinking agents include, e.g.,1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde,N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylicacid, homobifunctional imidoesters, including disuccinimidyl esters suchas 3,3′-dithiobis(succinimidylpropionate), bifunctional maleimides suchas bis-N-maleimido-1,8-octane and agents such asmethyl-3-[(p-azidophenyl)dithio]propioimidate.

Other modifications include deamidation of glutaminyl and asparaginylresidues to the corresponding glutamyl and aspartyl residues,respectively, hydroxylation of proline and lysine, phosphorylation ofhydroxyl groups of seryl, threonyl or tyrosyl residues, methylation ofthe α-amino groups of lysine, arginine, and histidine side chains [T. E.Creighton, Proteins: Structure and Molecular Properties, W.H. Freeman &Co., San Francisco, pp. 79-86 (1983)], acetylation of the N-terminalamine, and amidation of any C-terminal carboxyl group.

Another type of covalent modification of the cellular proliferationpolypeptide included within the scope of this invention comprisesaltering the native glycosylation pattern of the polypeptide. “Alteringthe native glycosylation pattern” is intended for purposes herein tomean deleting one or more carbohydrate moieties found in native sequencecellular proliferation polypeptide, and/or adding one or moreglycosylation sites that are not present in the native sequence cellularproliferation polypeptide.

Addition of glycosylation sites to cellular proliferation polypeptidesmay be accomplished by altering the amino acid sequence thereof. Thealteration may be made, for example, by the addition of, or substitutionby, one or more serine or threonine residues to the native sequencecellular proliferation polypeptide (for O-linked glycosylation sites).The cellular proliferation amino acid sequence may optionally be alteredthrough changes at the DNA level, particularly by mutating the DNAencoding the cellular proliferation polypeptide at preselected basessuch that codons are generated that will translate into the desiredamino acids.

Another means of increasing the number of carbohydrate moieties on thecellular proliferation polypeptide is by chemical or enzymatic couplingof glycosides to the polypeptide. Such methods are described in the art,e.g., in WO 87/05330 published 11 Sep. 1987, and in Aplin and Wriston,cellular proliferation Crit. Rev. Biochem., pp. 259-306 (1981).

Removal of carbohydrate moieties present on the cellular proliferationpolypeptide may be accomplished chemically or enzymatically or bymutational substitution of codons encoding for amino acid residues thatserve as targets for glycosylation. Chemical deglycosylation techniquesare known in the art and described, for instance, by Hakimuddin, et al.,Arch. Biochem. Biophys., 259:52 (1987) and by Edge et al., Anal.Biochem., 118:131 (1981). Enzymatic cleavage of carbohydrate moieties onpolypeptides can be achieved by the use of a variety of endo- andexo-glycosidases as described by Thotakura et al., Meth. Enzymol.,138:350 (1987).

Another type of covalent modification of cellular proliferationcomprises linking the cellular proliferation polypeptide to one of avariety of nonproteinaceous polymers, e.g., polyethylene glycol,polypropylene glycol, or polyoxyalkylenes, in the manner set forth inU.S. Pat. No. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or4,179,337.

The cellular proliferation polypeptides of the present invention mayalso be modified in one embodiment in a way to form chimeric moleculescomprising a cellular proliferation polypeptide fused to another,heterologous polypeptide or amino acid sequence. In one embodiment, sucha chimeric molecule comprises a fusion of a cellular proliferationpolypeptide with a tag polypeptide which provides an epitope to which ananti-tag antibody can selectively bind. Preferred tags include the mycepitope and 6-histidine. The epitope tag is generally placed at theamino- or carboxyl-terminus of the cellular proliferation polypeptide.The presence of such epitope-tagged forms of a cellular proliferationpolypeptide can be detected using an antibody against the tagpolypeptide as further discussed below. Also, provision of the epitopetag enables the cellular proliferation polypeptide to be readilypurified by affinity purification using an anti-tag antibody or anothertype of affinity matrix that binds to the epitope tag. In an alternativeembodiment, the chimeric molecule may comprise a fusion of a cellularproliferation polypeptide with an immunoglobulin or a particular regionof an immunoglobulin. For a bivalent form of the chimeric molecule, sucha fusion could be to the Fc region of an IgG molecule.

Various tag polypeptides and their respective antibodies are well knownin the art. Examples include poly-histidine (poly-his) orpoly-histidine-glycine (poly-his-gly) tags; the flu HA tag polypeptideand its antibody 12CA5 [Field et al., Mol. Cell. Biol., 8:2159-2165(1988)]; the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10antibodies thereto [Evan et al., Molecular and Cellular Biology,5:3610-3616 (1985)]; and the Herpes Simplex virus glycoprotein D (gD)tag and its antibody [Paborsky et al., Protein Engineering, 3(6):547-553(1990)]. Other tag polypeptides include the Flag-peptide [Hopp et al.,BioTechnology, 6:1204-1210 (1988)]; the KT3 epitope peptide [Martin etal., Science, 255:192-194 (1992)]; tubulin epitope peptide [Skinner etal., J. Biol. Chem., 266:15163-15166 (1991)]; and the T7 gene 10 proteinpeptide tag [Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA,87:6393-6397 (1990)].

Also included with the definition of cellular proliferation protein inone embodiment are other cellular proliferation proteins of the cellularproliferation family, and cellular proliferation proteins from otherorganisms, which are cloned and expressed as outlined below. Thus, probeor degenerate polymerase chain reaction (PCR) primer sequences may beused to find other related cellular proliferation proteins from humansor other organisms. As will be appreciated by those in the art,particularly useful probe and/or PCR primer sequences include the uniqueareas of the cellular proliferation nucleic acid sequence. As isgenerally known in the art, preferred PCR primers are from about 15 toabout 35 nucleotides in length, with from about 20 to about 30 beingpreferred, and may contain inosine as needed. The conditions for the PCRreaction are well known in the art.

In addition, as is outlined herein, cellular proliferation proteins canbe made that are longer than those depicted in the figures, for example,by the elucidation of additional sequences, the addition of epitope orpurification tags, the addition of other fusion sequences, etc.

Cellular proliferation proteins may also be identified as being encodedby cellular proliferation nucleic acids. Thus, in one embodiment,cellular proliferation proteins are encoded by nucleic acids that willhybridize to the sequences of the nucleic acid figures, or theircomplements, as outlined herein.

In a preferred embodiment, the cellular proliferation protein ispurified or isolated after expression. Cellular proliferation proteinsmay be isolated or purified in a variety of ways known to those skilledin the art depending on what other components are present in the sample.Standard purification methods include electrophoretic, molecular,immunological and chromatographic techniques, including ion exchange,hydrophobic, affinity, and reverse-phase HPLC chromatography, andchromatofocusing. For example, the cellular proliferation protein may bepurified using a standard anti-KSP antibody column. Ultrafiltration anddiafiltration techniques, in conjunction with protein concentration, arealso useful. For general guidance in suitable purification techniques,see Scopes, R., Protein Purification, Springer-Verlag, NY (1982). Thedegree of purification necessary will vary depending on the use of thecellular proliferation protein. In some instances no purification willbe necessary.

The terms “isolated” “purified” or “biologically pure” refer to materialthat is substantially or essentially free from components which normallyaccompany it as found in its native state. Purity and homogeneity aretypically determined using analytical chemistry techniques such aspolyacrylamide gel electrophoresis or high performance liquidchromatography. A protein that is the predominant species present in apreparation is substantially purified. The term “purified” denotes thata nucleic acid or protein gives rise to essentially one band in anelectrophoretic gel. Particularly, it means that the nucleic acid orprotein is at least 85% pure, more preferably at least 95% pure, andmost preferably at least 99% pure. In a preferred embodiment, a proteinis considered pure wherein it is determined that there is nocontaminating activity.

Once expressed and purified if necessary, the cellular proliferationproteins and nucleic acids are useful in a number of applications. In anumber of methods provided herein, wherein either the nucleic acid or aprotein is used, a candidate bioactive agent is used to determine theeffect on the cellular proliferation sequence, cellular proliferation,cancer, etc., as further discussed below.

In preferred embodiments, the bioactive agents modulate the cellularproliferation sequences or expression profiles provided herein. In aparticularly preferred embodiment, the candidate agent suppresses acellular proliferation phenotype, for example to inhibit proliferation,inhibit tumor growth, or to a normal tissue fingerprint as furtherdiscussed below. Similarly, the candidate agent preferably suppresses asevere cellular proliferation phenotype. Suppression might take the formof cell or tumor growth arrest, with continued viability. Alternatively,suppression may take the form of inducing cell death of cells, therebyeliminating proliferation. As further discussed below, preferredbioactive agents are identified which cause cell death selectively oftumor cells or proliferating cells. Generally a plurality of assaymixtures are run in parallel with different agent concentrations toobtain a differential response to the various concentrations. Typically,one of these concentrations serves as a negative control, i.e., at zeroconcentration or below the level of detection.

The term “candidate bioactive agent” or “drug candidate” or grammaticalequivalents as used herein describes any molecule, e.g., protein,oligopeptide, small organic molecule, polysaccharide, polynucleotide,purine analog, etc., to be tested for bioactive agents that are capableof directly or indirectly altering either the cellular proliferationphenotype or the expression of a cellular proliferation sequence,including both nucleic acid sequences and protein sequences. In othercases, alteration of cellular proliferation protein binding and/oractivity is screened. In the case where protein binding or activity isscreened, preferred embodiments exclude molecules already known to bindto that particular protein, for example, polymer structures such asmicrotubules, and energy sources such as ATP. Preferred embodiments ofassays herein include candidate agents which do not bind the cellularproliferation protein in its endogenous native state termed herein as“exogenous” agents. In another preferred embodiment, exogenous agentsfurther exclude antibodies to KSP.

Candidate agents can encompass numerous chemical classes, thoughtypically they are organic molecules, preferably small organic compoundshaving a molecular weight of more than 100 and less than about 2,500daltons. Small molecules are further defined herein as having amolecular weight of between 50 kD and 2000 kD. In another embodiment,small molecules have a molecular weight of less than 1500, or less than1200, or less than 1000, or less than 750, or less than 500 kD. In oneembodiment, a small molecule as used herein has a molecular weight ofabout 100 to 200 kD. Candidate agents comprise functional groupsnecessary for structural interaction with proteins, particularlyhydrogen bonding, and typically include at least an amine, carbonyl,hydroxyl or carboxyl group, preferably at least two of the functionalchemical groups. The candidate agents often comprise cyclical carbon orheterocyclic structures and/or aromatic or polyaromatic structuressubstituted with one or more of the above functional groups. Candidateagents are also found among biomolecules including peptides,saccharides, fatty acids, steroids, purines, pyrimidines, derivatives,structural analogs or combinations thereof. Particularly preferred arepeptides.

Candidate agents are obtained from a wide variety of sources includinglibraries of synthetic or natural compounds. For example, numerous meansare available for random and directed synthesis of a wide variety oforganic compounds and biomolecules, including expression of randomizedoligonucleotides. Alternatively, libraries of natural compounds in theform of bacterial, fungal, plant and animal extracts are available orreadily produced. Additionally, natural or synthetically producedlibraries and compounds are readily modified through conventionalchemical, physical and biochemical means. Known pharmacological agentsmay be subjected to directed or random chemical modifications, such asacylation, alkylation, esterification, amidification to producestructural analogs.

In a preferred embodiment, the candidate bioactive agents are proteins.By “protein” herein is meant at least two covalently attached aminoacids, which includes proteins, polypeptides, oligopeptides andpeptides. The protein may be made up of naturally occurring amino acidsand peptide bonds, or synthetic peptidomimetic structures. Thus “aminoacid”, or “peptide residue”, as used herein means both naturallyoccurring and synthetic amino acids. For example, homo-phenylalanine,citrulline and noreleucine are considered amino acids for the purposesof the invention. “Amino acid” also includes imino acid residues such asproline and hydroxyproline. The side chains may be in either the (R) orthe (S) configuration. In the preferred embodiment, the amino acids arein the (S) or L-configuration. If non-naturally occurring side chainsare used, non-amino acid substituents may be used, for example toprevent or retard in vivo degradations.

In a preferred embodiment, the candidate bioactive agents are naturallyoccurring proteins or fragments of naturally occurring proteins. Thus,for example, cellular extracts containing proteins, or random ordirected digests of proteinaceous cellular extracts, may be used. Inthis way libraries of procaryotic and eucaryotic proteins may be madefor screening in the methods of the invention. Particularly preferred inthis embodiment are libraries of bacterial, fungal, viral, and mammalianproteins, with the latter being preferred, and human proteins beingespecially preferred.

In a preferred embodiment, the candidate bioactive agents are peptidesof from about 5 to about 30 amino acids, with from about 5 to about 20amino acids being preferred, and from about 7 to about 15 beingparticularly preferred. The peptides may be digests of naturallyoccurring proteins as is outlined above, random peptides, or “biased”random peptides. By “randomized” or grammatical equivalents herein ismeant that each nucleic acid and peptide consists of essentially randomnucleotides and amino acids, respectively. Since generally these randompeptides (or nucleic acids, discussed below) are chemically synthesized,they may incorporate any nucleotide or amino acid at any position. Thesynthetic process can be designed to generate randomized proteins ornucleic acids, to allow the formation of all or most of the possiblecombinations over the length of the sequence, thus forming a library ofrandomized candidate bioactive proteinaceous agents.

In one embodiment, the library is fully randomized, with no sequencepreferences or constants at any position. In a preferred embodiment, thelibrary is biased. That is, some positions within the sequence areeither held constant, or are selected from a limited number ofpossibilities. For example, in a preferred embodiment, the nucleotidesor amino acid residues are randomized within a defined class, forexample, of hydrophobic amino acids, hydrophilic residues, stericallybiased (either small or large) residues, towards the creation of nucleicacid binding domains, the creation of cysteines, for cross-linking,prolines for SH-3 domains, serines, threonines, tyrosines or histidinesfor phosphorylation sites, etc., or to purines, etc.

In a preferred embodiment, the candidate bioactive agents are nucleicacids. By “nucleic acid” or “oligonucleotide” or grammatical equivalentsherein means at least two nucleotides covalently linked together. Anucleic acid of the present invention will generally containphosphodiester bonds, although in some cases, as outlined below, nucleicacid analogs are included that may have alternate backbones, comprising,for example, phosphoramide (Beaucage et al., Tetrahedron 49(10):1925(1993) and references therein; Letsinger, J. Org. Chem. 35:3800 (1970);Sprinzl et al., Eur. J. Biochem. 81:579 (1977); Letsinger et al., Nucl.Acids Res. 14:3487 (1986); Sawal et al, Chem. Lett. 805 (1984),Letsinger et al., J. Am. Chem. Soc. 110:4470 (1988); and Pauwels et al.,Chemica Scripta 26:141 91986)), phosphorothioate (Mag et al., NucleicAcids Res. 19:1437 (1991); and U.S. Pat. No. 5,644,048),phosphorodithioate (Briu et al., J. Am. Chem. Soc. 111:2321 (1989),O-methylphosphoroamidite linkages (see Eckstein, Oligonucleotides andAnalogues: A Practical Approach, Oxford University Press), and peptidenucleic acid backbones and linkages (see Egholm, J. Am. Chem. Soc.114:1895 (1992); Meier et al., Chem. Int. Ed. Engl. 31:1008 (1992);Nielsen, Nature, 365:566 (1993); Carlsson et al., Nature 380:207 (1996),all of which are incorporated by reference). Other analog nucleic acidsinclude those with positive backbones (Denpcy et al., Proc. Natl. Acad.Sci. USA 92:6097 (1995); non-ionic backbones (U.S. Pat. Nos. 5,386,023,5,637,684, 5,602,240, 5,216,141 and 4,469,863; Kiedrowshi et al., Angew.Chem. Intl. Ed. English 30:423 (1991); Letsinger et al., J. Am. Chem.Soc. 110:4470 (1988); Letsinger et al., Nucleoside & Nucleotide 13:1597(1994); Chapters 2 and 3, ASC Symposium Series 580, “CarbohydrateModifications in Antisense Research”, Ed. Y. S. Sanghui and P. Dan Cook;Mesmaeker et al., Bioorganic & Medicinal Chem. Lett. 4:395 (1994); Jeffset al., J. Biomolecular NMR 34:17 (1994); Tetrahedron Lett. 37:743(1996)) and non-ribose backbones, including those described in U.S. Pat.Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ASC Symposium Series580, “Carbohydrate Modifications in Antisense Research”, Ed. Y. S.Sanghui and P. Dan Cook. Nucleic acids containing one or morecarbocyclic sugars are also included within the definition of nucleicacids (see Jenkins et al., Chem. Soc. Rev. (1995) pp 169-176). Severalnucleic acid analogs are described in Rawls, C & E News Jun. 2, 1997page 35. All of these references are hereby expressly incorporated byreference. These modifications of the ribose-phosphate backbone may bedone to facilitate the addition of additional moieties such as labels,or to increase the stability and half-life of such molecules inphysiological environments. In addition, mixtures of naturally occurringnucleic acids and analogs can be made. Alternatively, mixtures ofdifferent nucleic acid analogs, and mixtures of naturally occurringnucleic acids and analogs may be made. The nucleic acids may be singlestranded or double stranded, as specified, or contain portions of bothdouble stranded or single stranded sequence. The nucleic acid may beDNA, both genomic and cDNA, RNA or a hybrid, where the nucleic acidcontains any combination of deoxyribo- and ribo-nucleotides, and anycombination of bases, including uracil, adenine, thymine, cytosine,guanine, inosine, xathanine hypoxathanine, isocytosine, isoguanine, etc.

As described above generally for proteins, nucleic acid candidatebioactive agents may be naturally occurring nucleic acids, randomnucleic acids, or “biased” random nucleic acids. For example, digests ofprocaryotic or eucaryotic genomes may be used as is outlined above forproteins.

In a preferred embodiment, the candidate bioactive agents are organicchemical moieties, a wide variety of which are available in theliterature.

In a preferred embodiment, as outlined above, screens may be done onindividual genes and gene products (proteins). In a preferredembodiment, the gene or protein has been identified as described belowas a differentially expressed gene important in a particular state.Thus, in one embodiment, screens are designed to first find candidateagents that can bind to differentially expressed proteins, and thenthese agents may be used in assays that evaluate the ability of thecandidate agent to modulate differentially expressed activity. Thus, aswill be appreciated by those in the art, there are a number of differentassays which may be run; binding assays and activity assays.

In a preferred embodiment, binding assays are provided. In oneembodiment, the methods comprise combining a cellular proliferationprotein and a candidate bioactive agent in the presence or absence ofmicrotubules, and determining the binding of the candidate agent to thecellular proliferation protein. Preferred embodiments utilize the humancellular proliferation protein, although other mammalian proteins mayalso be used as discussed above, for example for the development ofanimal models of human disease. In some embodiments, as outlined herein,variant or derivative cellular proliferation proteins may be used.

Generally, in a preferred embodiment of the methods herein, the cellularproliferation protein or the candidate agent is non-diffusably bound toan insoluble support having isolated sample receiving areas (e.g. amicrotiter plate, an array, etc.). The insoluble supports may be made ofany composition to which the compositions can be bound, is readilyseparated from soluble material, and is otherwise compatible with theoverall method of screening. The surface of such supports may be solidor porous and of any convenient shape. Examples of suitable insolublesupports include microtiter plates, arrays, membranes and beads. Theseare typically made of glass, plastic (e.g., polystyrene),polysaccharides, nylon or nitrocellulose, Teflon™, etc. Microtiterplates and arrays are especially convenient because a large number ofassays can be carried out simultaneously, using small amounts ofreagents and samples. The particular manner of binding of thecomposition is not crucial so long as it is compatible with the reagentsand overall methods of the invention, maintains the activity of thecomposition and is nondiffusable. Preferred methods of binding includethe use of antibodies (which do not sterically block either the ligandbinding site or activation sequence when the protein is bound to thesupport), direct binding to “sticky” or ionic supports, chemicalcrosslinking, the synthesis of the protein or agent on the surface, etc.Following binding of the protein or agent, excess unbound material isremoved by washing. The sample receiving areas may then be blockedthrough incubation with bovine serum albumin (BSA), casein or otherinnocuous protein or other moiety.

In a preferred embodiment, the cellular proliferation protein is boundto the support, and, in the presence or absence of microtubules, acandidate bioactive agent is added to the assay. Alternatively, thecandidate agent is bound to the support and the cellular proliferationprotein is added. Novel binding agents include specific antibodies,non-natural binding agents identified in screens of chemical libraries,peptide analogs, etc. A wide variety of assays may be used for thispurpose, including labeled in vitro protein-protein binding assays,electrophoretic mobility shift assays, immunoassays for protein binding,functional assays (phosphorylation assays, etc.) and the like. Moreover,in another aspect, screening assays are performed herein where neitherthe drug candidate nor cellular proliferation protein are bound to asolid support. Soluble assays are known in the art. In one embodiment,binding of a cellular proliferation protein, or fragment thereof, to adrug candidate can be determined by changes in fluorescence of eitherthe cellular proliferation protein or the drug candidate, or both.Fluorescence may be intrinsic or conferred by labeling either componentwith a fluorophor. As an example that is not meant to be limiting,binding could be detected by fluorescence polarization.

The determination of the binding of the candidate bioactive agent to thecellular proliferation protein may be done in a number of ways. In apreferred embodiment, the candidate bioactive agent is labelled, andbinding determined directly. For example, this may be done by attachingall or a portion of the cellular proliferation protein to a solidsupport, adding a labelled candidate agent (for example a fluorescentlabel), washing off excess reagent, and determining whether the label ispresent on the solid support. Various blocking and washing steps may beutilized as is known in the art.

By “labeled” herein is meant that the compound is either directly orindirectly labeled with a label which provides a detectable signal, e.g.radioisotope, fluorofers including organo-metallic fluorescentcompounds, enzyme, antibodies, particles such as magnetic particles,chemiluminescers, or specific binding molecules, etc. Specific bindingmolecules include pairs, such as biotin and streptavidin, digoxin andantidigoxin etc. For the specific binding members, the complementarymember would normally be labeled with a molecule which provides fordetection, in accordance with known procedures, as outlined above. Thelabel can directly or indirectly provide a detectable signal.

In some embodiments, only one of the components is labeled. For example,the proteins (or proteinaceous candidate agents) may be labeled attyrosine positions using ¹²⁵I, or with fluorophores. Alternatively, morethan one component may be labeled with different labels; using ¹²⁵I forthe proteins, for example, and a fluorophor for the candidate agents.

In a preferred embodiment, the binding of the candidate bioactive agentis determined through the use of competitive binding assays. In thisembodiment, the competitor is a binding moiety known to bind to thetarget molecule (i.e. cellular proliferation protein), such as ATP,microtubules, an antibody, peptide; binding partner, ligand, etc. Undercertain circumstances, there may be competitive binding as between thebioactive agent and the binding moiety, with the binding moietydisplacing the bioactive agent.

In one embodiment, the candidate bioactive agent is labeled. Either thecandidate bioactive agent, or the competitor, or both, is added first tothe protein for a time sufficient to allow binding, if present.Incubations may be performed at any temperature which facilitatesoptimal activity, typically between 4 and 40° C. Incubation periods areselected for optimum activity, but may also be optimized to facilitaterapid high through put screening. Typically between 0.1 and 1 hour willbe sufficient. Excess reagent is generally removed or washed away. Thesecond component is then added, and the presence or absence of thelabeled component is followed, to indicate binding.

In a preferred embodiment, the competitor is added first, followed bythe candidate bioactive agent. Displacement of the competitor is anindication that the candidate bioactive agent is binding to the cellularproliferation protein and thus is capable of binding to, and potentiallymodulating, the activity of the cellular proliferation protein. In thisembodiment, either component can be labeled. Thus, for example, if thecompetitor is labeled, the presence of label in the wash solutionindicates displacement by the agent. Alternatively, if the candidatebioactive agent is labeled, the presence of the label on the supportindicates displacement.

In an alternative embodiment, the candidate bioactive agent is addedfirst, with incubation and washing, followed by the competitor. Theabsence of binding by the competitor may indicate that the bioactiveagent is bound to the cellular proliferation protein with a higheraffinity. Thus, if the candidate bioactive agent is labeled, thepresence of the label on the support, coupled with a lack of competitorbinding, may indicate that the candidate agent is capable of binding tothe cellular proliferation protein.

In another aspect herein, proteins which bind to KSP or a fragmentthereof are identified. Genetic systems have been described to detectprotein-protein interactions. The first work was done in yeast systems,namely the “yeast two-hybrid” system. The basic system requires aprotein-protein interaction in order to turn on transcription of areporter gene. Subsequent work was done in mammalian cells. See Fieldset al., Nature 340:245 (1989); Vasavada et al., PNAS USA 88:10686(1991); Fearon et al., PNAS USA 89:7958 (1992); Dang et al., Mol. Cell.Biol. 11:954 (1991); Chien et al., PNAS USA 88:9578 (1991); and U.S.Pat. Nos. 5,283,173, 5,667,973, 5,468,614, 5,525,490, and 5,637,463.

In a preferred embodiment, the binding site of the cellularproliferation protein is identified and provided herein. This can bedone in a variety of ways. For example, once the cellular proliferationprotein has been identified as binding to a bioactive agent, the proteinis fragmented or modified and the assays repeated to identify thenecessary components for binding.

In a preferred embodiment, the methods comprise differential screeningto identify bioactive agents that are capable of modulating the activityof the cellular proliferation proteins. In this embodiment, the methodscomprise combining a cellular proliferation protein and a competitor ina first sample. A second sample comprises a candidate bioactive agent, acellular proliferation protein and a competitor. The binding of thecompetitor is determined for both samples, and a change, or differencein binding between the two samples indicates the presence of an agentcapable of binding to the cellular proliferation protein and, in oneembodiment, modulating its activity. Methods of determining modulationof activity are further described below. That is, if the binding of thecompetitor is different in the second sample relative to the firstsample, the agent is capable of binding to the cellular proliferationprotein.

Alternatively, a preferred embodiment utilizes differential screening toidentify drug candidates that, in the presence or absence ofmicrotubules, bind to the native cellular proliferation protein, butcannot bind to modified cellular proliferation proteins. The structureof the cellular proliferation protein may be modeled, and used inrational drug design to synthesize agents that interact with that site.Drug candidates that affect cellular proliferation bioactivity are alsoidentified by screening drugs for the ability to either enhance orreduce the activity of the protein in the presence or absence ofmicrotubules.

Positive controls and negative controls may be used in the assays.Preferably all control and test samples are performed in at leasttriplicate to obtain statistically significant results. Incubation ofall samples is for a time sufficient for the binding of the agent to theprotein. Following incubation, all samples are washed free ofnon-specifically bound material and the amount of bound, generallylabeled agent determined. For example, where a radiolabel is employed,the samples may be counted in a scintillation counter to determine theamount of bound compound.

A variety of other reagents may be included in the screening assays.These include reagents like salts, neutral proteins, e.g. albumin,detergents, etc which may be used to facilitate optimal protein-proteinbinding and/or reduce non-specific or background interactions. Alsoreagents that otherwise improve the efficiency of the assay, such asprotease inhibitors, nuclease inhibitors, anti-microbial agents, etc.,may be used. The mixture of components may be added in any order thatprovides for the requisite binding.

Screening for agents that modulate the activity of cellularproliferation proteins may also be done. In a preferred embodiment,methods for screening for a bioactive agent capable of modulating theactivity of cellular proliferation proteins comprise the steps of addinga candidate bioactive agent to a sample of cellular proliferationproteins in the presence or absence of microtubules, as above, anddetermining an alteration in the biological activity of cellularproliferation proteins. “Modulating the activity of cellularproliferation” includes an increase in activity, a decrease in activity,or a change in the type or kind of activity present. Thus, in thisembodiment, the candidate agent should both bind to cellularproliferation proteins (although this may not be necessary), and alterits biological or biochemical activity as defined herein. The methodsinclude both in vitro screening methods, as are generally outlinedabove, and in vivo screening of cells for alterations in the presence,distribution, activity or amount of cellular proliferation proteins.

Thus, in this embodiment, the methods comprise combining a cellularproliferation sample and a candidate bioactive agent, and evaluating theeffect on cellular proliferation activity. By “cellular proliferationprotein activity” or grammatical equivalents herein is meant at leastone of the cellular proliferation protein's biological activities,including, but not limited to, kinesin activity, regulation of spindlepole separation, mitosis, mitotic spindle assembly, satisfaction of themitotic cell cycle checkpoint, cell cycle progression, apoptosis, cellproliferation, mitotic and involvement in tumor growth. An inhibitor ofcellular proliferation activity is the inhibition of any one or morecellular proliferation protein activities.

Kinesin activity is known in the art and includes one or more kinesinactivities. Kinesin activities include the ability to affect ATPhydrolysis, microtubule binding, gliding andpolymerization/depolymerization (effects on microtubule dynamics),binding to other proteins of the spindle, binding to proteins involvedin cell-cycle control, or serving as a substrate to other enzymes, suchas kinases or proteases and specific kinesin cellular activities such asspindle separation.

Methods of performing motility assays are well known to those of skillin the art (see, e.g., Hall, et al. (1996), Biophys. J., 71: 3467-3476,Turner et al., 1996, Anal. Biochem. 242 (1):20-5; Gittes et al., 1996,Biophys. J. 70(1): 418-29; Shirakawa et al., 1995, J. Exp. Biol. 198:1809-15; Winkelmann et al., 1995, Biophys. J. 68: 2444-53; Winkelmann etal., 1995, Biophys. J. 68: 72S, and the like).

In addition to the assays described above, methods known in the art fordetermining ATPase activity can be used. Preferably, solution basedassays are utilized. Alternatively, conventional methods are used. Forexample, P, release from kinesin can be quantified. In one preferredembodiment, the ATPase activity assay utilizes 0.3 M PCA (perchloricacid) and malachite green reagent (8.27 mM sodium molybdate II, 0.33 mMmalachite green oxalate, and 0.8 mM Triton X-100). To perform the assay,10 μL of reaction is quenched in 90 μL of cold 0.3 M PCA. Phosphatestandards are used so data can be converted to mM inorganic phosphatereleased. When all reactions and standards have been quenched in PCA,100 μL of malachite green reagent is added to the to relevant wells ine.g., a microtiter plate. The mixture is developed for 10-15 minutes andthe plate is read at an absorbance of 650 nm. If phosphate standardswere used, absorbance readings can be converted to mM P, and plottedover time. Additionally, ATPase assays known in the art include theluciferase assay.

In another preferred method, kinesin activity is measured by the methodsdisclosed in Ser. No. 09/314,464, filed May 18, 1999, entitled,Compositions and Assay Utilizing ADP or Phosphate for Detecting ProteinModulators.

In a preferred embodiment, the activity of the cellular proliferationprotein is increased; in another preferred embodiment, the activity ofthe cellular proliferation protein is decreased. Thus, bioactive agentsthat are antagonists are preferred in some embodiments, and bioactiveagents that are agonists may be preferred in other embodiments.

In one aspect of the invention, cells containing cellular proliferationsequences are used in drug screening assays by evaluating the effect ofdrug candidates on cellular proliferation. Cell type include normalcells, and more preferably cells with abnormal proliferative ratesincluding tumor cells, most preferably human tumor cells. Methods ofassessing cellular proliferation are known in the art and include growthand viability assays using cultured cells. In such assays, cellpopulations are monitored for growth and or viability, often over timeand comparing samples incubated with various concentrations of thebioactive agent or without the bioactive agent. Cell number can bequantified using agents that such as3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolim bromide (MTT),3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium(MTS) [U.S. Pat. No. 5,185,450] and Alamar Blue which are converted tocolored or fluorescent compounds in the presence of metabolically activecells. Alternatively, dyes that bind to cellular protein such assulforhodamine B (SRB) or crystal violet can be used to quantify cellnumber. Alternatively, cells can be directly counted using a particlecounter, such as a Coulter Counter® manufactured by Beckman Coulter, orcounted using a microscope to observe cells on a hemocytometer.Preferably, cells counted using the hemocytometer are observed in asolution of trypan blue to distinguish viable from dead cells. Othermethods of quantifying cell number are known to those skilled in theart. These assays can be performed on any of the cells, including thosein a state of necrosis.

Moreover, apoptosis can be determined by methods known in the art. Forexample, markers for apoptosis are known, and TUNEL (TdT-mediateddUTP-fluorescein nick end labeling) kits can be bought commercially, forexample, Boehringer Mannheim kit, catalog no. 168795.

In a preferred embodiment, the methods comprise adding a candidatebioactive agent, as defined above, to a cell comprising cellularproliferation proteins. Preferred cell types include almost any cell.The cells contain a nucleic acid, preferably recombinant, that encodes acellular proliferation protein. In a preferred embodiment, a library ofcandidate agents are tested on a plurality of cells.

In one aspect, the assays are evaluated in the presence or absence orprevious or subsequent exposure to physiological signals, for examplehormones, antibodies, peptides, antigens, cytokines, growth factors,action potentials, pharmacological agents including chemotherapeutics,radiation, carcinogenics, or other cells (i.e. cell-cell contacts). Inanother example, the determinations are determined at different stagesof the cell cycle process.

In one aspect of the invention, the cellular proliferation sequences andcells containing cellular proliferation sequences are used in drugscreening assays by evaluating the effect of drug candidates on a “geneexpression profile” or expression profile genes. In a preferredembodiment, the expression profiles are used, preferably in conjunctionwith high throughput screening techniques to allow monitoring forexpression profile genes after treatment with a candidate agent. See,Zlokarnik, et al., Science 279, 84-8 (1998).

In one aspect, the expression levels of genes are determined fordifferent cellular states in the cellular proliferation phenotype; thatis, the expression levels of genes in normal tissue in proliferating andnon-proliferating states, and in abnormal cellular proliferation tissue(and in some cases, for varying seventies of cellular proliferation thatrelate to prognosis, as outlined below) are evaluated to provideexpression profiles. Abnormal states include cancer states and otherhyper or hypo proliferation states as further defined below.

An expression profile of a particular cell state or point of developmentis essentially a “fingerprint” of the state; while two states may haveany particular gene similarly expressed, the evaluation of a number ofgenes simultaneously allows the generation of a gene expression profilethat is unique to the state of the cell. By comparing expressionprofiles of cells in different states, information regarding which genesare important (including both up- and down-regulation of genes) in eachof these states is obtained. Then, diagnosis may be done or confirmed:does tissue from a particular patient have the gene expression profileof normal or abnormal cellular proliferation tissue.

“Differential expression,” or grammatical equivalents as used herein,refers to both qualitative as well as quantitative differences in thegenes' temporal and/or cellular expression patterns within and among thecells. Thus, a differentially expressed gene can qualitatively have itsexpression altered, including an activation or inactivation, in, forexample, normal versus abnormal cellular proliferation tissue. That is,genes may be turned on or turned off in a particular state, relative toanother state or have a different timing pattern, for example, cancerouscells may have genes which stay on. As is apparent to the skilledartisan, any comparison of two or more states can be made and repeatedat various time points. Such a qualitatively regulated gene will exhibitan expression pattern within a state or cell type which is detectable bystandard techniques in one such state or cell type, but is notdetectable in both. Alternatively, the determination is quantitative inthat expression is increased or decreased: that is, the expression ofthe gene is either upregulated, resulting in an increased amount oftranscript, or downregulated, resulting in a decreased amount oftranscript. The degree to which expression differs need only be largeenough to quantify via standard characterization techniques as outlinedbelow, such as by use of Affymetrix GeneChip™ expression arrays,Lockhart, Nature Biotechnology, 14:1675-1680 (1996), hereby expresslyincorporated by reference. Other techniques include, but are not limitedto, quantitative reverse transcriptase PCR, Northern analysis and RNaseprotection. As outlined above, preferably the change in expression (i.e.upregulation or downregulation) is at least about 50%, more preferablyat least about 100%, more preferably at least about 150%, morepreferably, at least about 200%, with from 300 to at least 1000% beingespecially preferred.

As will be appreciated by those in the art, this may be done byevaluation at either the gene transcript, or the protein level; that is,the amount of gene expression may be monitored using nucleic acid probesto the DNA or RNA equivalent of the gene transcript, and thequantification of gene expression levels, or, alternatively, the finalgene product itself (protein) can be monitored, for example through theuse of antibodies to the cellular proliferation protein and standardimmunoassays (ELISAs, etc.) or other techniques, including massspectroscopy assays, 2D gel electrophoresis assays, etc. Thus, theproteins corresponding to cellular proliferation genes, i.e. thoseidentified as being important in a cellular proliferation phenotype, canbe evaluated in a cellular proliferation diagnostic test.

In a preferred embodiment nucleic acids encoding the cellularproliferation protein are detected. Although DNA or RNA encoding thecellular proliferation protein may be detected, of particular interestare methods wherein the mRNA encoding a cellular proliferation proteinis detected. The presence of mRNA in a sample is an indication that thecellular proliferation gene has been transcribed to form the mRNA, andsuggests that the protein is expressed. Probes to detect the mRNA can beany nucleotide/deoxynucleotide probe that is complementary to and basepairs with the mRNA and includes but is not limited to oligonucleotides,cDNA or RNA. Probes also should contain a detectable label, as definedherein. In one method the mRNA is detected after immobilizing thenucleic acid to be examined on a solid support such as nylon membranesand hybridizing the probe with the sample. Following washing to removethe non-specifically bound probe, the label is detected. In anothermethod detection of the mRNA is performed in situ. In this methodpermeabilized cells or tissue samples are contacted with a detectablylabeled nucleic acid probe for sufficient time to allow the probe tohybridize with the target mRNA. Following washing to remove thenon-specifically bound probe, the label is detected. For example adigoxygenin labeled riboprobe (RNA probe) that is complementary to themRNA encoding a cellular proliferation protein is detected by bindingthe digoxygenin with an anti-digoxygenin secondary antibody anddeveloped with nitro blue tetrazolium and 5-bromo-4-chloro-3-indoylphosphate.

In one case, having identified a particular gene as up regulated incellular proliferation, candidate bioactive agents may be screened tomodulate this gene's response; preferably to down regulate the gene,although in some circumstances to up regulate the gene. “Modulation”thus includes both an increase and a decrease in gene expression or achange in temporal pattern. The preferred amount of modulation willdepend on the original change of the gene expression in normal versustumor tissue, with changes of at least 10%, preferably 50%, morepreferably 100-300%, and in some embodiments 300-1000% or greater. Thus,if a gene exhibits a 4 fold increase in tumor compared to normal tissue,a decrease of about four fold is desired; a 10 fold decrease in tumorcompared to normal tissue gives a 10 fold increase in expression for acandidate agent is desired.

In a preferred embodiment, gene expression monitoring is done and anumber of genes, i.e. an expression profile, is monitoredsimultaneously, although multiple protein expression monitoring can bedone as well.

In one embodiment, the cellular proliferation nucleic acid probes areattached to biochips as outlined below for the detection andquantification of cellular proliferation sequences in a particular cell.

Generally, in a preferred embodiment, a candidate bioactive agent isadded to the cells prior to analysis. Any cell can be used, includingnormal and abnormal cells, including tumor and non-tumor mammalian,preferably human cells. In some cases, plant cells are used. After thecandidate agent has been added and the cells allowed to incubate forsome period of time, the sample containing the target sequences to beanalyzed is added to the biochip. If required, the target sequence isprepared using known techniques. For example, the sample may be treatedto lyse the cells, using known lysis buffers, electroporation, etc.,with purification and/or amplification such as PCR occurring as needed,as will be appreciated by those in the art. For example, an in vitrotranscription with labels covalently attached to the nucleosides isdone. Generally, the nucleic acids are labeled with biotin-FITC or PE,or with cy3 or cy5.

In a preferred embodiment, the target sequence is labeled with, forexample, a fluorescent, a chemiluminescent, a chemical, or a radioactivesignal, to provide a means of detecting the target sequence's specificbinding to a probe. The label also can be an enzyme, such as, alkalinephosphatase or horseradish peroxidase, which when provided with anappropriate substrate produces a product that can be detected.Alternatively, the label can be a labeled compound or small molecule,such as an enzyme inhibitor, that binds but is not catalyzed or alteredby the enzyme. The label also can be a moiety or compound, such as, anepitope tag or biotin which specifically binds to streptavidin. For theexample of biotin, the streptavidin is labeled as described above,thereby, providing a detectable signal for the bound target sequence. Asknown in the art, unbound labeled streptavidin is removed prior toanalysis.

As will be appreciated by those in the art, these assays can be directhybridization assays or can comprise “sandwich assays”, which includethe use of multiple probes, as is generally outlined in U.S. Pat. Nos.5,681,702, 5,597,909, 5,545,730, 5,594,117, 5,591,584, 5,571,670,5,580,731, 5,571,670, 5,591,584, 5,624,802, 5,635,352, 5,594,118,5,359,100, 5,124,246 and 5,681,697, all of which are hereby incorporatedby reference. In this embodiment, in general, the target nucleic acid isprepared as outlined above, and then added to the biochip comprising aplurality of nucleic acid probes, under conditions that allow theformation of a hybridization complex.

A variety of hybridization conditions may be used in the presentinvention, including high, moderate and low stringency conditions asoutlined above. The assays are generally run under stringency conditionswhich allows formation of the label probe hybridization complex only inthe presence of target. Stringency can be controlled by altering a stepparameter that is a thermodynamic variable, including, but not limitedto, temperature, formamide concentration, salt concentration, chaotropicsalt concentration pH, organic solvent concentration, etc.

These parameters may also be used to control non-specific binding, as isgenerally outlined in U.S. Pat. No. 5,681,697. Thus it may be desirableto perform certain steps at higher stringency conditions to reducenon-specific binding.

The reactions outlined herein may be accomplished in a variety of ways,as will be appreciated by those in the art. Components of the reactionmay be added simultaneously, or sequentially, in any order, withpreferred embodiments outlined below. In addition, the reaction mayinclude a variety of other reagents may be included in the assays. Theseinclude reagents like salts, buffers, neutral proteins, e.g. albumin,detergents, etc which may be used to facilitate optimal hybridizationand detection, and/or reduce non-specific or background interactions.Also reagents that otherwise improve the efficiency of the assay, suchas protease inhibitors, nuclease inhibitors, anti-microbial agents,etc., may be used, depending on the sample preparation methods andpurity of the target.

Once the assay is run, the data is analyzed to determine the expressionlevels, and changes in expression levels as between states, ofindividual genes, forming a gene expression profile.

In one aspect, the screens are done to identify drugs or bioactiveagents that modulate the cellular proliferation phenotype. Specifically,there are several types of screens that can be run. A preferredembodiment is in the screening of candidate agents that can induce orsuppress a particular expression profile, thus preferably generating theassociated phenotype. That is, candidate agents that can mimic orproduce an expression profile in cellular proliferation similar to theexpression profile of normal non-cancerous tissue is expected to resultin a suppression of the cellular proliferation phenotype. Thus, in thisembodiment, mimicking an expression profile, or changing one profile toanother, is the goal.

In a preferred embodiment, as for the diagnosis and prognosisapplications discussed below, having identified the differentiallyexpressed genes important in any one state as further described below,screens can be run to alter the expression of the genes individually.That is, screening for modulation of regulation of expression of asingle gene can be done that is, rather than try to mimic all or part ofan expression profile, screening for regulation of individual genes canbe done. Thus, for example, particularly in the case of target geneswhose presence, absence or temporal pattern is unique between twostates, screening is done for modulators of the target gene expression.In a preferred embodiment, the target gene encodes the cellularproliferation protein described herein. Thus, screening of candidateagents that modulate the cellular proliferation phenotype either at thegene expression level or the protein level can be done.

In addition screens can be done for novel genes that are induced inresponse to a candidate agent. After identifying a candidate agent basedupon its ability to suppress a cellular proliferation expression patternleading to a normal expression pattern, or modulate a single cellularproliferation gene expression profile so as to mimic the expression ofthe gene from normal tissue, a screen as described above can beperformed to identify genes that are specifically modulated in responseto the agent. Comparing expression profiles between normal tissue andagent treated cellular proliferation tissue reveals genes that are notexpressed in normal tissue or cellular proliferation tissue, but areexpressed in agent treated tissue. These agent specific sequences can beidentified and used by any of the methods described herein for cellularproliferation genes or proteins. In particular these sequences and theproteins they encode find use in marking or identifying agent treatedcells. In addition, antibodies can be raised against the agent inducedproteins and used to target novel therapeutics to the treated cellularproliferation tissue sample.

In one embodiment, a candidate agent is administered to a population ofcellular proliferation cells, that thus has an associated Cellularproliferation expression profile. By “administration” or “contacting”herein is meant that the candidate agent is added to the cells in such amanner as to allow the agent to act upon the cell, whether by uptake andintracellular action, or by action at the cell surface. In someembodiments, nucleic acid encoding a proteinaceous candidate agent (i.e.a peptide) may be put into a viral construct such as a retroviralconstruct and added to the cell, such that expression of the peptideagent is accomplished; see PCT US97/01019, hereby expressly incorporatedby reference. The phrase “under conditions which allow the cell touptake the candidate agent” means that the cell is biologically involvedin the uptake and intracellular action, or by action at the cell surfacein that the agent is not injected into the cell. It is understood thattargeting ligands and biochemically agents can be used to facilitate theuptake, however, this differs from mechanical injection. Mechanicalinjection is explicitly excluded from the definition of “taken up by thecell” as used herein, and is excluded from conditions inductive to highthroughput assays as used herein:

Once the candidate agent has been administered to the cells, the cellscan be washed if desired and are allowed to incubate under preferablyphysiological conditions for some period of time. The cells are thenharvested and a new gene expression profile is generated, as outlinedherein.

Thus, for example, cellular proliferation tissue may be screened foragents that reduce or suppress the cellular proliferation phenotype. Achange in at least one gene of the expression profile indicates that theagent has an effect on cellular proliferation activity. By defining sucha signature for the cellular proliferation phenotype, screens for newdrugs that alter the phenotype can be devised. With this approach, thedrug target need not be known and need not be represented in theoriginal expression screening platform, nor does the level of transcriptfor the target protein need to change.

In all the methods provided herein, bioactive agents are identified.Similarly, compounds which interfere with binding or interaction betweenthe cellular proliferation protein and an identified binding ormodulating agent can be identified. Moreover, transgenic models asdiscussed below may be used to identify bioactive agents. Compounds withpharmacological activity are able to enhance or interfere with theactivity of the cellular proliferation protein. The compounds can beused in further assays so as to confirm activity wherein necessary oroptimize conditions including varying the identified molecules. In apreferred embodiment, the agents are used as therapeutics as discussedbelow.

In a further aspect of the present invention, methods of modulatingcellular proliferation in cells or organisms are provided. In oneembodiment, the methods comprise administering to a cell ananti-cellular proliferation antibody as further discussed below thatreduces or eliminates the biological activity of an endogeneous cellularproliferation protein. In a preferred embodiment, a nucleic acidencoding said antibody is administered. Agents identified to modulatecellular proliferation can also be used. Alternatively, the methodscomprise administering to a cell or organism a composition comprising acellular proliferation sequence.

In a preferred embodiment, for example when the cellular proliferationsequence is down-regulated in cellular proliferation, the activity ofthe cellular proliferation gene is increased by increasing the amount ofcellular proliferation in the cell, for example by overexpressing theendogeneous cellular proliferation or by administering a gene encodingthe cellular proliferation sequence, using known gene-therapytechniques, for example. In a preferred embodiment, the gene therapytechniques include the incorporation of the exogeneous gene usingenhanced homologous recombination (EHR), for example as described inPCT/US93/03868, hereby incorporated by reference in its entirety.Alternatively, for example when the cellular proliferation sequence isup-regulated in cellular proliferation, the activity of the endogeneouscellular proliferation gene is decreased, for example by theadministration of a cellular proliferation antisense nucleic acid.Preferably, as discussed below, cellular proliferation is inhibited.

Thus, In one embodiment, a method of inhibiting cell division isprovided. In a preferred embodiment, a method of inhibiting tumor growthis provided. In a further embodiment, methods of treating cells orindividuals with cancer are provided. The method comprisesadministration of a cellular proliferation inhibitor.

In one embodiment, a cellular proliferation inhibitor is an antibody asdiscussed above and further described below. In another embodiment, thecellular proliferation inhibitor is an antisense molecule as discussedabove. Antisense molecules as used herein include antisense or senseoligonucleotides comprising a singe-stranded nucleic acid sequence(either RNA or DNA) capable of binding to target mRNA (sense) or DNA(antisense) sequences for cellular proliferation molecules. A preferredantisense molecule is for KSP or for a ligand or activator thereof.Antisense or sense oligonucleotides, according to the present invention,comprise a fragment generally at least about 14 nucleotides, preferablyfrom about 14 to 30 nucleotides. The ability to derive an antisense or asense oligonucleotide, based upon a cDNA sequence encoding a givenprotein is described in, for example, Stein and Cohen (Cancer Res.48:2659, 1988) and van der Krol et al. (BioTechniques 6:958, 1988).

Antisense molecules may be introduced into a cell containing the targetnucleotide sequence by formation of a conjugate with a ligand bindingmolecule, as described in WO 91/04753. Suitable ligand binding moleculesinclude, but are not limited to, cell surface receptors, growth factors,other cytokines, or other ligands that bind to cell surface receptors.Preferably, conjugation of the ligand binding molecule does notsubstantially interfere with the ability of the ligand binding moleculeto bind to its corresponding molecule or receptor, or block entry of thesense or antisense oligonucleotide or its conjugated version into thecell. Alternatively, a sense or an antisense oligonucleotide may beintroduced into a cell containing the target nucleic acid sequence byformation of an oligonucleotide-lipid complex, as described in WO90/10448. It is understood that the use of antisense molecules or knockout and knock in models may also be used in screening assays asdiscussed above, in addition to methods of treatment. Moreover, knockout models can include knocking out expression, rather than the genome,such as by the use ribozymes. In one case, ribozymes are a preferred KSPinhibitor.

As discussed above, the methods and compositions herein are not limitedto cancer. Disease states which can be treated by the methods andcompositions provided herein include, but are not limited to, cancer(further discussed below), restenosis, autoimmune disease, arthritis,graft rejection, inflammatory bowel disease, proliferation induced aftermedical procedures, including, but not limited to, surgery, angioplasty,and the like. It is appreciated that in some cases the cells may not bein a hyper or hypo proliferation state (abnormal state) and stillrequire treatment. For example, during wound healing, the cells may beproliferating “normally”, but proliferation enhancement may be desired.Similarly, as discussed above, in the agriculture arena, cells may be ina “normal” state, but proliferation modulation may be desired to enhancea crop by directly enhancing growth of a crop, or by inhibiting thegrowth of a plant or organism which adversely affects the crop. Thus, inone embodiment, the invention herein includes application to cells orindividuals afflicted or impending affliction with any one of thesedisorders or states.

The compositions and methods provided herein are particularly deemeduseful for the treatment of cancer including solid tumors such as skin,breast, brain, cervical carcinomas, testicular carcinomas, etc. Moreparticularly, cancers that may be treated by the compositions andmethods of the invention include, but are not limited to: Cardiac:sarcoma (angiosarcoma, fibrosarcoma, rhabdomyosarcoma, liposarcoma),myxoma, rhabdomyoma, fibroma, lipoma and teratoma; Log: bronchogeniccarcinoma (squamous cell, undifferentiated small cell, undifferentiatedlarge cell, adenocarcinoma), alveolar (bronchiolar) carcinoma, bronchialadenoma, sarcoma, lymphoma, chondromatous hamartoma, mesothelioma;Gastrointestinal: esophagus (squamous cell carcinoma, adenocarcinoma,leiomyosarcoma, lymphoma), stomach (carcinoma, lymphoma,leiomyosarcoma), pancreas (ductal adenocarcinoma, insulinoma,glucagonoma, gastrinoma, carcinoid tumors, vipoma), small bowel(adenocarcinoma, lymphoma, carcinoid tumors, Karposi's sarcoma,leiomyoma, hemangioma, lipoma, neurofibroma, fibroma), large bowel(adenocarcinoma, tubular adenoma, villous adenoma, hamartoma,leiomyoma); Genitourinary tract: kidney (adenocarcinoma, calm's tumor[nephroblastoma], lymphoma, leukemia), bladder and urethra (squamouscell carcinoma, transitional cell carcinoma, adenocarcinoma), prostate(adenocarcinoma, sarcoma), testis (seminoma, teratoma, embryonalcarcinoma, teratocarcinoma, choriocarcinoma, sarcoma, interstitial cellcarcinoma, fibroma, fibroadenoma, adenomatoid tumors, lipoma); Liver:hepatoma (hepatocellular carcinoma), cholangiocarcinoma, hepatoblastom,angiosarcoma, hepatocellular adenoma, hemangioma; Bone: osteogenicsarcoma (osteosarcoma), fibrosarcoma, malignant fibrous histiocytoma,chondrosarcoma, Ewing's sarcoma, malignant lymphoma (reticulum cellsarcoma), multiple myeloma, malignant giant cell tumor chordoma,osteochronfroma (osteocartilaginous exostoses), benign chondroma,chondroblastoma, chondromyxofibroma, osteoid osteoma and giant celltumors; Nervous system: skull (osteoma, hemangioma, granuloma, xanthoma,osteitis deformans), meninges (meningioma, meningiosarcoma,gliomatosis); brain (astrocytoma, medulloblastoma, glioma, ependymoma,germinoma [pinealoma], glioblastoma multiform, oligodendroglioma,schwannoma, retinoblastoma, congenital tumors), spinal cordneurofibroma, meningioma, glioma, sarcoma); Gynecological: uterus(endometrial carcinoma), cervix (cervical carcinoma, pre-tumor cervicaldysplasia), ovaries (ovarian carcinoma [serous cystadenocarcinoma,mucinous cystadenocarcinoma, unclassified carcinoma], granulosa-thecalcell tumors, Sertoli-Leydig cell tumors, dysgerminoma, malignantteratoma), vulva (squamous cell carcinoma, intraepithelial carcinoma,adenocarcinoma, fibrosarcoma, melanoma), vagina (clear cell carcinoma,squamous cell carcinoma, botryoid sarcoma [embryonal rhabdomyosarcoma],fallopian tubes (carcinoma); Hematologic: blood (myeloid leukemia [acuteand chronic], acute lymphoblastic leukemia, chronic lymphocyticleukemia, myeloproliferative diseases, multiple myeloma, myelodysplasticsyndrome), Hodgkin's disease, non-Hodgkin's lymphoma [malignantlymphoma]; Skin: malignant melanoma, basal cell carcinoma, squamous cellcarcinoma, Karposi's sarcoma, moles dysplastic nevi, lipoma, angioma,dermatofibroma, keloids, psoriasis; and Adrenal glands: neuroblastoma.The cancer can be solid tumors or metastatic. Thus, the term “cancerouscell” as provided herein, includes a cell afflicted by any one of theabove identified conditions.

In another aspect herein, diagnostic assays are provided herein. In oneembodiment, the cellular proliferation sequences are used in thediagnostic assays. This can be done on an individual gene orcorresponding polypeptide level. In a preferred embodiment, theexpression profiles are used, preferably in conjunction with highthroughput screening techniques to allow monitoring for expressionprofile genes and/or corresponding polypeptides. In a preferredembodiment in situ hybridization of labeled cellular proliferationnucleic acid probes to tissue arrays is done. For example, arrays oftissue samples, including cellular proliferation tissue in variousstates and or time points and/or normal tissue, are made. In situhybridization as is known in the art can then be done. It is understoodthat conventional antibody and protein localization methods can also beused in diagnostic assays herein.

It is understood that when comparing the fingerprints between anindividual and a standard, the skilled artisan can make a diagnosis aswell as a prognosis. It is further understood that the genes whichindicate the diagnosis may differ from those which indicate theprognosis.

In a preferred embodiment, the cellular proliferation sequences are usedin prognosis assays. As above, gene expression profiles can be generatedthat correlate to cellular proliferation severity, in terms of long termprognosis. Again, this may be done on either a protein or gene level,with the use of genes being preferred. In both the diagnostic andprognostic assays, the cellular proliferation probes can be attached tobiochips as described below for the detection and quantification ofcellular proliferation sequences in a tissue or patient.

Accordingly, disorders based on mutant or variant cellular proliferationgenes may also be determined. In one embodiment, the invention providesmethods for identifying cells containing variant cellular proliferationgenes comprising determining all or part of the sequence of at least oneendogenous cellular proliferation genes in a cell. As will beappreciated by those in the art, this may be done using any number ofsequencing techniques. In a preferred embodiment, the invention providesmethods of identifying the cellular proliferation genotype of anindividual comprising determining all or part of the sequence of atleast one cellular proliferation gene of the individual. This isgenerally done in at least one tissue of the individual, and may includethe evaluation of a number of tissues or different samples of the sametissue. The method may include comparing the sequence of the sequencedcellular proliferation gene to a known cellular proliferation gene, i.e.a wild-type gene.

The sequence of all or part of the cellular proliferation gene can thenbe compared to the sequence of a known cellular proliferation gene todetermine if any differences exist. This can be done using any number ofknown homology programs, such as Bestfit, etc. In a preferredembodiment, the presence of a difference in the sequence between thecellular proliferation gene of the patient and the known cellularproliferation gene is indicative of a disease state or a propensity fora disease state, as outlined herein.

In a preferred embodiment, the cellular proliferation genes are used asprobes to determine the number of copies of the cellular proliferationgene in the genome.

In another preferred embodiment cellular proliferation genes are used asprobes to determine the chromosomal localization of the cellularproliferation genes. Information such as chromosomal localization findsuse in providing a diagnosis or prognosis in particular when chromosomalabnormalities such as translocations, and the like are identified incellular proliferation gene loci.

Once a determination has been made regarding the proliferation state ofa cell, if desired, the compositions or agents described herein can beadministered. The compounds having the desired pharmacological activitymay be administered in a physiologically acceptable carrier (also calleda pharmaceutically acceptable carrier) to a host. Depending upon themanner of introduction, the compounds may be formulated in a variety ofways as discussed below. The concentration of therapeutically activecompound in the formulation may vary from about 0.1-100 wt. %. Theagents may be administered alone or in combination with othertreatments, e.g., radiation.

Thus, in a preferred embodiment, cellular proliferation proteins andmodulators are administered as therapeutic agents. Similarly, cellularproliferation genes (including both the full-length sequence, partialsequences, or regulatory sequences of the cellular proliferation codingregions) can be administered in gene therapy applications, as is knownin the art. These cellular proliferation genes can include antisenseapplications, either as gene therapy (i.e. for incorporation into thegenome) or as antisense compositions, as will be appreciated by those inthe art.

In the preferred embodiment, the pharmaceutical compositions are in awater soluble form, such as being present as pharmaceutically acceptablesalts, which is meant to include both acid and base addition salts.“Pharmaceutically acceptable acid addition salt” refers to those saltsthat retain the biological effectiveness of the free bases and that arenot biologically or otherwise undesirable, formed with inorganic acidssuch as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid,phosphoric acid and the like, and organic acids such as acetic acid,propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid,malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid,benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid,ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid and thelike. “Pharmaceutically acceptable base addition salts” include thosederived from inorganic bases such as sodium, potassium, lithium,ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminumsalts and the like. Particularly preferred are the ammonium, potassium,sodium, calcium, and magnesium salts. Salts derived frompharmaceutically acceptable organic non-toxic bases include salts ofprimary, secondary, and tertiary amines, substituted amines includingnaturally occurring substituted amines, cyclic amines and basic ionexchange resins, such as isopropylamine, trimethylamine, diethylamine,triethylamine, tripropylamine, and ethanolamine.

The pharmaceutical compositions can be prepared in various forms, suchas granules, tablets, pills, suppositories, capsules, suspensions,salves, lotions and the like. Pharmaceutical grade organic or inorganiccarriers and/or diluents suitable for oral and topical use can be usedto make up compositions containing the therapeutically-active compounds.Diluents known to the art include aqueous media, vegetable and animaloils and fats. Stabilizing agents, wetting and emulsifying agents, saltsfor varying the osmotic pressure or buffers for securing an adequate pHvalue, and skin penetration enhancers can be used as auxiliary agents.The pharmaceutical compositions may also include one or more of thefollowing: carrier proteins such as serum albumin; buffers; fillers suchas microcrystalline cellulose, lactose, corn and other starches; bindingagents; sweeteners and other flavoring agents; coloring agents; andpolyethylene glycol. Additives are well known in the art, and are usedin a variety of formulations.

The administration of the cellular proliferation proteins and modulatorsof the present invention can be done in a variety of ways as discussedabove, including, but not limited to, orally, subcutaneously,intravenously, intranasally, transdermally, intraperitoneally,intramuscularly, intrapulmonary, vaginally, rectally, or intraocularly.In some instances, for example, in the treatment of wounds andinflammation, the cellular proliferation proteins and modulators may bedirectly applied as a solution or spray.

In one embodiment, a therapeutically effective dose of a cellularproliferation protein or modulator thereof is administered to a patient.By “therapeutically effective dose” herein is meant a dose that producesthe effects for which it is administered. The exact dose will depend onthe purpose of the treatment, and will be ascertainable by one skilledin the art using known techniques. As is known in the art, adjustmentsfor cellular proliferation degradation, systemic versus localizeddelivery, and rate of new protease synthesis, as well as the age, bodyweight, general health, sex, diet, time of administration, druginteraction and the severity of the condition may be necessary, and willbe ascertainable with routine experimentation by those skilled in theart.

a “patient” for the purposes of the present invention includes bothhumans and other animals, particularly mammals, and organisms. Thus themethods are applicable to both human therapy and veterinaryapplications. In the preferred embodiment the patient is a mammal, andin the most preferred embodiment the patient is human.

In a preferred embodiment, cellular proliferation genes are administeredas DNA vaccines, either single genes or combinations of cellularproliferation genes. Naked DNA vaccines are generally known in the art.Brower, Nature Biotechnology, 16:1304-1305 (1998).

In one embodiment, cellular proliferation genes of the present inventionare used as DNA vaccines. Methods for the use of genes as DNA vaccinesare well known to one of ordinary skill in the art, and include placinga cellular proliferation gene or portion of a cellular proliferationgene under the control of a promoter for expression in a cellularproliferation patient. The cellular proliferation gene used for DNAvaccines can encode full-length cellular proliferation proteins, butmore preferably encodes portions of the cellular proliferation proteinsincluding peptides derived from the cellular proliferation protein. In apreferred embodiment a patient is immunized with a DNA vaccinecomprising a plurality of nucleotide sequences derived from a cellularproliferation gene. Similarly, it is possible to immunize a patient witha plurality of cellular proliferation genes or portions thereof asdefined herein. Without being bound by theory, expression of thepolypeptide encoded by the DNA vaccine, cytotoxic T-cells, helperT-cells and antibodies are induced which recognize and destroy oreliminate cells expressing cellular proliferation proteins.

In a preferred embodiment, the DNA vaccines include a gene encoding anadjuvant molecule with the DNA vaccine. Such adjuvant molecules includecytokines that increase the immunogenic response to the cellularproliferation polypeptide encoded by the DNA vaccine. Additional oralternative adjuvants are known to those of ordinary skill in the artand find use in the invention.

In another preferred embodiment cellular proliferation genes find use ingenerating animal models of cellular proliferation. As is appreciated byone of ordinary skill in the art, when the cellular proliferation geneidentified is repressed or diminished in cellular proliferation tissue,gene therapy technology wherein antisense RNA directed to the cellularproliferation gene will also diminish or repress expression of the gene.An animal generated as such serves as an animal model of cellularproliferation that finds use in screening bioactive drug candidates.Similarly, gene knockout technology, for example as a result ofhomologous recombination with an appropriate gene targeting vector, willresult in the absence of the cellular proliferation protein. Whendesired, tissue-specific expression or knockout of the cellularproliferation protein may be necessary.

It is also possible that the cellular proliferation protein isoverexpressed in cellular proliferation. As such, transgenic animals canbe generated that overexpress the cellular proliferation protein.Depending on the desired expression level, promoters of variousstrengths can be employed to express the transgene. Also, the number ofcopies of the integrated transgene can be determined and compared for adetermination of the expression level of the transgene. Animalsgenerated by such methods find use as animal models of cellularproliferation and are additionally useful in screening for bioactivemolecules to treat cellular proliferation.

In a preferred embodiment, biochips are provided herein. Nucleic acidprobes to cellular proliferation nucleic acids (both the nucleic acidsequences outlined in the figures and/or the complements thereof) aremade. The nucleic acid probes attached to the biochip are designed to besubstantially complementary to the cellular proliferation nucleic acids,i.e. the target sequence (either the target sequence of the sample or toother probe sequences, for example in sandwich assays), such thathybridization of the target sequence and the probes of the presentinvention occurs. As outlined below, this complementarity need not beperfect; there may be any number of base pair mismatches which willinterfere with hybridization between the target sequence and the singlestranded nucleic acids of the present invention. However, if the numberof mutations is so great that no hybridization can occur under even theleast stringent of hybridization conditions, the sequence is not acomplementary target sequence. Thus, by “substantially complementary”herein is meant that the probes are sufficiently complementary to thetarget sequences to hybridize under normal reaction conditions,particularly high stringency conditions, as outlined herein.

A nucleic acid probe is generally single stranded but can be partiallysingle and partially double stranded. The strandedness of the probe isdictated by the structure, composition, and properties of the targetsequence. In general, the nucleic acid probes range from about 8 toabout 100 bases long, with from about 10 to about 80 bases beingpreferred, and from about 30 to about 50 bases being particularlypreferred. That is, generally whole genes are not used. In someembodiments, much longer nucleic acids can be used, up to hundreds ofbases.

In a preferred embodiment, more than one probe per sequence is used,with either overlapping probes or probes to different sections of thetarget being used. That is, two, three, four or more probes, with threebeing preferred, are used to build in a redundancy for a particulartarget. The probes can be overlapping (i.e. have some sequence incommon), or separate.

As will be appreciated by those in the art, nucleic acids can beattached or immobilized to a solid support in a wide variety of ways. By“immobilized” and grammatical equivalents herein is meant theassociation or binding between the nucleic acid probe and the solidsupport is sufficient to be stable under the conditions of binding,washing, analysis, and removal as outlined below. The binding can becovalent or non-covalent. By “non-covalent binding” and grammaticalequivalents herein is meant one or more of either electrostatic,hydrophilic, and hydrophobic interactions. Included in non-covalentbinding is the covalent attachment of a molecule, such as, streptavidinto the support and the non-covalent binding of the biotinylated probe tothe streptavidin. By “covalent binding” and grammatical equivalentsherein is meant that the two moieties, the solid support and the probe,are attached by at least one bond, including sigma bonds, pi bonds andcoordination bonds. Covalent bonds can be formed directly between theprobe and the solid support or can be formed by a cross linker or byinclusion of a specific reactive group on either the solid support orthe probe or both molecules. Immobilization may also involve acombination of covalent and non-covalent interactions.

In general, the probes are attached to the biochip in a wide variety ofways, as will be appreciated by those in the art. As described herein,the nucleic acids can either be synthesized first, with subsequentattachment to the biochip, or can be directly synthesized on thebiochip.

The biochip comprises a suitable solid substrate. By “substrate” or“solid support” or other grammatical equivalents herein is meant anymaterial that can be modified to contain discrete individual sitesappropriate for the attachment or association of the nucleic acid probesand is amenable to at least one detection method. As will be appreciatedby those in the art, the number of possible substrates are very large,and include, but are not limited to, glass and modified orfunctionalized glass, plastics (including acrylics, polystyrene andcopolymers of styrene and other materials, polypropylene, polyethylene,polybutylene, polyurethanes, TeflonJ, etc.), polysaccharides, nylon ornitrocellulose, resins, silica or silica-based materials includingsilicon and modified silicon, carbon, metals, inorganic glasses,plastics, etc. In general, the substrates allow optical detection and donot appreciably fluorescese. a preferred substrate is described incopending application entitled Reusable Low Fluorescent Plastic Biochipfiled Mar. 15, 1999, herein incorporated by reference in its entirety.

Generally the substrate is planar, although as will be appreciated bythose in the art, other configurations of substrates may be used aswell. For example, the probes may be placed on the inside surface of atube, for flow-through sample analysis to minimize sample volume.Similarly, the substrate may be flexible, such as a flexible foam,including closed cell foams made of particular plastics.

In a preferred embodiment, the surface of the biochip and the probe maybe derivatized with chemical functional groups for subsequent attachmentof the two. Thus, for example, the biochip is derivatized with achemical functional group including, but not limited to, amino groups,carboxy groups, oxo groups and thiol groups, with amino groups beingparticularly preferred. Using these functional groups, the probes can beattached using functional groups on the probes. For example, nucleicacids containing amino groups can be attached to surfaces comprisingamino groups, for example using linkers as are known in the art; forexample, homo- or hetero-bifunctional linkers as are well known (see1994 Pierce Chemical Company catalog, technical section oncross-linkers, pages 155-200, incorporated herein by reference). Inaddition, in some cases, additional linkers, such as alkyl groups(including substituted and heteroalkyl groups) may be used.

In this embodiment, the oligonucleotides are synthesized as is known inthe art, and then attached to the surface of the solid support. As willbe appreciated by those skilled in the art, either the 5′ or 3′ terminusmay be attached to the solid support, or attachment may be via aninternal nucleoside.

In an additional embodiment, the immobilization to the solid support maybe very strong, yet non-covalent. For example, biotinylatedoligonucleotides can be made, which bind to surfaces covalently coatedwith streptavidin, resulting in attachment.

Alternatively, the oligonucleotides may be synthesized on the surface,as is known in the art. For example, photoactivation techniquesutilizing photopolymerization compounds and techniques are used. In apreferred embodiment, the nucleic acids can be synthesized in situ,using well known photolithographic techniques, such as those describedin WO 95/25116; WO 95/35505; U.S. Pat. Nos. 5,700,637 and 5,445,934; andreferences cited within, all of which are expressly incorporated byreference; these methods of attachment form the basis of the AffimetrixGeneChip™ technology.

In another preferred embodiment anti-cellular proliferation antibodiesare provided. In one case, the cellular proliferation protein is to beused to generate antibodies, for example for immunotherapy. Wherein afragment of the cellular proliferation protein is used, the cellularproliferation protein should share at least one epitope or determinantwith the full length protein. By “epitope” or “determinant” herein ismeant a portion of a protein which will generate and/or bind an antibodyor T-cell receptor in the context of MHC. Thus, in most instances,antibodies made to a smaller cellular proliferation protein will be ableto bind to the full length protein. In a preferred embodiment, theepitope is unique; that is, antibodies generated to a unique epitopeshow little or no cross-reactivity.

In one embodiment, the term “antibody” includes antibody fragments, asare known in the art, including Fab, Fab₂, single chain antibodies (Fvfor example), chimeric antibodies, etc., either produced by themodification of whole antibodies or those synthesized de novo usingrecombinant DNA technologies.

Methods of preparing polyclonal antibodies are known to the skilledartisan. Polyclonal antibodies can be raised in a mammal, for example,by one or more injections of an immunizing agent and, if desired, anadjuvant. Typically, the immunizing agent and/or adjuvant will beinjected in the mammal by multiple subcutaneous or intraperitonealinjections. The immunizing agent may include the KSP or fragment thereofor a fusion protein thereof. It may be useful to conjugate theimmunizing agent to a protein known to be immunogenic in the mammalbeing immunized. Examples of such immunogenic proteins include but arenot limited to keyhole limpet hemocyanin, serum albumin, bovinethyroglobulin, and soybean trypsin inhibitor. Examples of adjuvantswhich may be employed include Freund's complete adjuvant and MPL-TDMadjuvant (monophosphoryl Lipid a, synthetic trehalose dicorynomycolate).The immunization protocol may be selected by one skilled in the artwithout undue experimentation.

The antibodies may, alternatively, be monoclonal antibodies. Monoclonalantibodies may be prepared using hybridoma methods, such as thosedescribed by Kohler and Milstein, Nature, 256:495 (1975). In a hybridomamethod, a mouse, hamster, or other appropriate host animal, is typicallyimmunized with an immunizing agent to elicit lymphocytes that produce orare capable of producing antibodies that will specifically bind to theimmunizing agent. Alternatively, the lymphocytes may be immunized invitro. The immunizing agent will typically include the KSP polypeptideor fragment thereof or a fusion protein thereof. Generally, eitherperipheral blood lymphocytes (“PBLs”) are used if cells of human originare desired, or spleen cells or lymph node cells are used if non-humanmammalian sources are desired. The lymphocytes are then fused with animmortalized cell line using a suitable fusing agent, such aspolyethylene glycol, to form a hybridoma cell [Goding MonoclonalAntibodies: Principles and practice, Academic Press, (1986) pp. 59-103].Immortalized cell lines are usually transformed mammalian cells,particularly myeloma cells of rodent, bovine and human origin. Usually,rat or mouse myeloma cell lines are employed. The hybridoma cells may becultured in a suitable culture medium that preferably contains one ormore substances that inhibit the growth or survival of the unfused,immortalized cells. For example, if the parental cells lack the enzymehypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT), theculture medium for the hybridomas typically will include hypoxanthine,aminopterin, and thymidine (“HAT medium”), which substances prevent thegrowth of HGPRT-deficient cells.

In one embodiment, the antibodies are bispecific antibodies. Bispecificantibodies are monoclonal, preferably human or humanized, antibodiesthat have binding specificities for at least two different antigens. Inthe present case, one of the binding specificities is for the KSP or afragment thereof, the other one is for any other antigen, and preferablyfor a cell-surface protein or receptor or receptor subunit, preferablyone that is tumor specific.

In a preferred embodiment, the antibodies to cellular proliferation arecapable of reducing or eliminating the biological function of cellularproliferation, as is described below. That is, the addition of anti-KSPantibodies (either polyclonal or preferably monoclonal) to cellularproliferation (or cells containing cellular proliferation) may reduce oreliminate the cellular proliferation activity. Generally, at least a 25%decrease in activity is preferred, with at least about 50% beingparticularly preferred and about a 95-100% decrease being especiallypreferred.

In a preferred embodiment the antibodies to the cellular proliferationproteins are humanized antibodies. Humanized forms of non-human (e.g.,murine) antibodies are chimeric molecules of immunoglobulins,immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′,F(ab′)₂ or other antigen-binding subsequences of antibodies) whichcontain minimal sequence derived from non-human immunoglobulin.Humanized antibodies include human immunoglobulins (recipient antibody)in which residues form a complementary determining region (CDR) of therecipient are replaced by residues from a CDR of a non-human species(donor antibody) such as mouse, rat or rabbit having the desiredspecificity, affinity and capacity. In some instances, Fv frameworkresidues of the human immunoglobulin are replaced by correspondingnon-human residues. Humanized antibodies may also comprise residueswhich are found neither in the recipient antibody nor in the importedCDR or framework sequences. In general, the humanized antibody willcomprise substantially all of at least one, and typically two, variabledomains, in which all or substantially all of the CDR regions correspondto those of a non-human immunoglobulin and all or substantially all ofthe FR regions are those of a human immunoglobulin consensus sequence.The humanized antibody optimally also will comprise at least a portionof an immunoglobulin constant region (Fc), typically that of a humanimmunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann etal., Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol.,2:593-596 (1992)].

Methods for humanizing non-human antibodies are well known in the art.Generally, a humanized antibody has one or more amino acid residuesintroduced into it from a source which is non-human. These non-humanamino acid residues are often referred to as import residues, which aretypically taken from an import variable domain. Humanization can beessentially performed following the method of Winter and co-workers[Jones et al., Nature 321:522-525 (1986); Riechmann et al., Nature332:323-327 (1988); Verhoeyen et al. Science, 239:1534-1536 (1988)], bysubstituting rodent CDRs or CDR sequences for the correspondingsequences of a human antibody. Accordingly, such humanized antibodiesare chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantiallyless than an intact human variable domain has been substituted by thecorresponding sequence from a non-human species. In practice, humanizedantibodies are typically human antibodies in which some CDR residues andpossibly some FR residues are substituted by residues from analogoussites in rodent antibodies.

Human antibodies can also be produced using various techniques known inthe art, including phage display libraries [Hoogenboom and Winter, J.Mol. Biol. 227:381 (1991); Marks et al., J. Mol. Biol., 222:581 (1991)].The techniques of Cole et al. and Boerner et al. are also available forthe preparation of human monoclonal antibodies (Cole et al., MonoclonalAntibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985) and Boerner etal., J. Immunol., 147(1):86-95 (1991)). Similarly, human antibodies canbe made by introducing of human immunoglobulin loci into transgenicanimals, e.g., mice in which the endogenous immunoglobulin genes havebeen partially or completely inactivated. Upon challenge, human antibodyproduction is observed, which closely resembles that seen in humans inall respects, including gene rearrangement, assembly, and antibodyrepertoire. This approach is described, for example, in U.S. Pat. Nos.5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016, and inthe following scientific publications: Marks et al., Bio/Technology 10,779-783 (1992); Lonberg et al., Nature 368 856-859 (1994); MorrisonNature 368, 812-13 (1994); Fishwild et al., Nature Biotechnology 14,845-51 (1996); Neuberger, Nature Biotechnology 14, 826 (1996); Lonbergand Huszar, Intern. Rev. Immunol. 13 65-93 (1995).

By immunotherapy is meant treatment of cellular proliferation with anantibody raised against cellular proliferation proteins. As used herein,immunotherapy can be passive or active. Passive immunotherapy as definedherein is the passive transfer of antibody to a recipient (patient).Active immunization is the induction of antibody and/or T-cell responsesin a recipient (patient). Induction of an immune response is the resultof providing the recipient with an antigen to which antibodies areraised. As appreciated by one of ordinary skill in the art, the antigenmay be provided by injecting a polypeptide against which antibodies aredesired to be raised into a recipient, or contacting the recipient witha nucleic acid capable of expressing the antigen and under conditionsfor expression of the antigen.

As will be appreciated by one of ordinary skill in the art, the antibodymay be a competitive, non-competitive or uncompetitive inhibitor ofprotein binding to the cellular proliferation protein. Preferably, theantibody is also an antagonist of the cellular proliferation protein. Inone aspect, when the antibody prevents the binding of other molecules tothe cellular proliferation protein, the antibody prevents growth of thecell. The antibody also sensitizes the cell to cytotoxic agents,including, but not limited to TNF-α, TNF-β, IL-1, INF-γ and IL-2, orchemotherapeutic agents including 5FU, vinblastine, actinomycin D,cisplatin, methotrexate, and the like.

In another preferred embodiment, the antibody is conjugated to atherapeutic moiety. In one aspect the therapeutic moiety is a smallmolecule that modulates the activity of the cellular proliferationprotein. In another aspect the therapeutic moiety modulates the activityof molecules associated with or in close proximity to the cellularproliferation protein.

In a preferred embodiment, the therapeutic moiety may also be acytotoxic agent. In this method, targeting the cytotoxic agent to tumortissue or cells, results in a reduction in the number of afflictedcells, thereby reducing symptoms associated with cellular proliferation.Cytotoxic agents are numerous and varied and include, but are notlimited to, cytotoxic drugs or toxins or active fragments of suchtoxins. Suitable toxins and their corresponding fragments includediptheria a chain, exotoxin a chain, ricin a chain, abrin a chain,curcin, crotin, phenomycin, enomycin and the like. Cytotoxic agents alsoinclude radiochemicals made by conjugating radioisotopes to antibodiesraised against cellular proliferation proteins, or binding of aradionuclide to a chelating agent that has been covalently attached tothe antibody. Targeting the therapeutic moiety to cellular proliferationproteins not only serves to increase the local concentration oftherapeutic moiety in the cellular proliferation afflicted area, butalso serves to reduce deleterious side effects that may be associatedwith the therapeutic moiety.

Preferably, the antibody is conjugated to a protein which facilitatesentry into the cell. In one case, the antibody enters the cell byendocytosis. In another embodiment, a nucleic acid encoding the antibodyis administered to the individual or cell. The nucleic acid isidentified based on the sequence of the antibody, determined by standardrecombinant techniques. Moreover, wherein the cellular proliferationprotein can be targeted within a cell, i.e., the nucleus, an antibodythereto contains a signal for that target localization, i.e., a nuclearlocalization signal.

In a preferred embodiment, the cellular proliferation antibodies of theinvention specifically bind to cellular proliferation proteins. By“specifically bind” herein is meant that the antibodies bind to theprotein with a binding constant in the range of at least 10⁻⁴-10⁻⁸ M⁻¹,with a preferred range being 10⁻⁷-10⁻⁹ M⁻¹.

It is understood that the examples described above in no way serve tolimit the true scope of this invention, but rather are presented forillustrative purposes. All references cited herein are incorporated byreference in their entirety as well as the sequences cited therein orhaving a GenBank accession number.

1-33. (canceled)
 34. A method of evaluating a hyper-proliferativedisorder comprising: (a) determining the level of expression ofkindle-like spindle protein (KSP) in a sample from a tissue having thehyper-proliferative disorder; and (b) comparing said KSP expressionlevel to a standard or control level of expression, wherein an increaseindicates that the hyper-proliferative disorder is KSP-mediated.
 35. Themethod of claim 34 wherein said hyper-proliferative disorder is cancer.36-59. (canceled)
 60. The method of claim 34, wherein the sample isselected from the group consisting of a blood sample, a urine sample, abuccal sample, a PAP smear, a cerebral spinal fluid sample, a breasttissue sample, a lung tissue sample, and a colon tissue sample.
 61. Themethod of claim 34, wherein the standard or control level isrepresentative of normal cells not in a hyper-proliferative state. 62.The method of claim 61, wherein the hyper-proliferative disorder iscancer, and step (b) is performed by nucleic acid hybridization.
 63. Themethod of claim 34, wherein step (a) further comprises determining theexpression level of at least one additional cell proliferation protein;and step (b) comprises the expression levels of each cell proliferationprotein with the expression level of the same protein in the standard orcontrol level.
 64. The method of claim 63, wherein the additional cellproliferation protein is a kinesin.
 65. The method of claim 63, whereinthe standard or control level for each cell proliferation protein isrepresentative of normal cells not in a hyper-proliferative state. 66.The method of claim 65, wherein the hyper-proliferative disorder iscancer.
 67. The method of claim 34, wherein step (a) comprisesdetermining the amount of nucleic acid encoding KSP in the sample. 68.The method of claim 67, wherein the amount of nucleic acid encoding KSPis determined by nucleic acid hybridization.
 69. The method of claim 67,wherein the nucleic acid hybridization is in situ hybridization.
 70. Themethod of claim 67, wherein the nucleic acid is DNA.
 71. The method ofclaim 67, wherein the nucleic acid is RNA.
 72. The method of claim 34,wherein step (a) comprises determining the amount of KSP protein in thesample.
 73. The method of claim 72, wherein the amount of KSP protein isdetermined by mass spectroscopy.
 74. The method of claim 72, wherein theamount of KSP protein is determined by an immunological method.
 75. Themethod of claim 74, wherein the immunological method is an enzyme-linkedimmunoassay (ELISA).
 76. The method of claim 72, wherein the amount ofKSP protein is determined by two-dimensional gel electrophoresis. 77.The method of claim 34, further comprising the step of administering atherapeutically effective amount of a KSP inhibitor, when an increase isdetected in step (b).
 78. The method of claim 77, wherein thehyper-proliferative disorder is cancer.
 79. The method of claim 77,wherein the KSP inhibitor is a small molecule having a molecular weightof between 50 kD and 2000 kD.